(53f08330) · Commits · 郑智淋 / lammps

doc/Section_commands.txt

+4 −0

Original line number	Diff line number	Diff line
		@@ -521,9 +521,11 @@ g = GPU, i = USER-INTEL, k = KOKKOS, o = USER-OMP, t = OPT.
		"nph (ko)"_fix_nh.html,
		"nphug (o)"_fix_nphug.html,
		"nph/asphere (o)"_fix_nph_asphere.html,
		"nph/body"_fix_nph_body.html,
		"nph/sphere (o)"_fix_nph_sphere.html,
		"npt (ckio)"_fix_nh.html,
		"npt/asphere (o)"_fix_npt_asphere.html,
		"npt/body"_fix_npt_body.html,
		"npt/sphere (o)"_fix_npt_sphere.html,
		"nve (ckio)"_fix_nve.html,
		"nve/asphere (i)"_fix_nve_asphere.html,
		@@ -536,6 +538,7 @@ g = GPU, i = USER-INTEL, k = KOKKOS, o = USER-OMP, t = OPT.
		"nve/tri"_fix_nve_tri.html,
		"nvt (ciko)"_fix_nh.html,
		"nvt/asphere (o)"_fix_nvt_asphere.html,
		"nvt/body"_fix_nvt_body.html,
		"nvt/sllod (io)"_fix_nvt_sllod.html,
		"nvt/sphere (o)"_fix_nvt_sphere.html,
		"oneway"_fix_oneway.html,
		@@ -719,6 +722,7 @@ KOKKOS, o = USER-OMP, t = OPT.
		"stress/atom"_compute_stress_atom.html,
		"temp (ck)"_compute_temp.html,
		"temp/asphere"_compute_temp_asphere.html,
		"temp/body"_compute_temp_body.html,
		"temp/chunk"_compute_temp_chunk.html,
		"temp/com"_compute_temp_com.html,
		"temp/deform"_compute_temp_deform.html,

doc/fix_nph_body.html

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		<div class="section" id="fix-nph-body-command">
		<span id="index-0"></span><h1>fix nph/body command<a class="headerlink" href="#fix-nph-body-command" title="Permalink to this headline">¶</a></h1>
		<div class="section" id="syntax">
		<h2>Syntax<a class="headerlink" href="#syntax" title="Permalink to this headline">¶</a></h2>
		<div class="highlight-python"><div class="highlight"><pre>fix ID group-ID nph/body args keyword value ...
		</pre></div>
		</div>
		<ul class="simple">
		<li>ID, group-ID are documented in <a class="reference internal" href="fix.html"><em>fix</em></a> command</li>
		<li>nph/body = style name of this fix command</li>
		<li>additional barostat related keyword/value pairs from the <a class="reference internal" href="fix_nh.html"><em>fix nph</em></a> command can be appended</li>
		</ul>
		</div>
		<div class="section" id="examples">
		<h2>Examples<a class="headerlink" href="#examples" title="Permalink to this headline">¶</a></h2>
		<div class="highlight-python"><div class="highlight"><pre>fix 1 all nph/body iso 0.0 0.0 1000.0
		fix 2 all nph/body x 5.0 5.0 1000.0
		fix 2 all nph/body x 5.0 5.0 1000.0 drag 0.2
		fix 2 water nph/body aniso 0.0 0.0 1000.0 dilate partial
		</pre></div>
		</div>
		</div>
		<div class="section" id="description">
		<h2>Description<a class="headerlink" href="#description" title="Permalink to this headline">¶</a></h2>
		<p>Perform constant NPH integration to update position, velocity,
		orientation, and angular velocity each timestep for body
		particles in the group using a Nose/Hoover pressure
		barostat. P is pressure; H is enthalpy. This creates a system
		trajectory consistent with the isenthalpic ensemble.</p>
		<p>This fix differs from the <a class="reference internal" href="fix_nh.html"><em>fix nph</em></a> command, which assumes
		point particles and only updates their position and velocity.</p>
		<p>Additional parameters affecting the barostat are specified by keywords
		and values documented with the <a class="reference internal" href="fix_nh.html"><em>fix nph</em></a> command. See,
		for example, discussion of the <em>aniso</em>, and <em>dilate</em> keywords.</p>
		<p>The particles in the fix group are the only ones whose velocities and
		positions are updated by the velocity/position update portion of the
		NPH integration.</p>
		<p>Regardless of what particles are in the fix group, a global pressure is
		computed for all particles. Similarly, when the size of the simulation
		box is changed, all particles are re-scaled to new positions, unless the
		keyword <em>dilate</em> is specified with a value of <em>partial</em>, in which case
		only the particles in the fix group are re-scaled. The latter can be
		useful for leaving the coordinates of particles in a solid substrate
		unchanged and controlling the pressure of a surrounding fluid.</p>
		<hr class="docutils" />
		<p>This fix computes a temperature and pressure each timestep. To do
		this, the fix creates its own computes of style “temp/body” and
		“pressure”, as if these commands had been issued:</p>
		<div class="highlight-python"><div class="highlight"><pre>compute fix-ID_temp all temp/body
		compute fix-ID_press all pressure fix-ID_temp
		</pre></div>
		</div>
		<p>See the <a class="reference internal" href="compute_temp_body.html"><em>compute temp/body</em></a> and <a class="reference internal" href="compute_pressure.html"><em>compute pressure</em></a> commands for details. Note that the
		IDs of the new computes are the fix-ID + underscore + “temp” or fix_ID
		+ underscore + “press”, and the group for the new computes is “all”
		since pressure is computed for the entire system.</p>
		<p>Note that these are NOT the computes used by thermodynamic output (see
		the <a class="reference internal" href="thermo_style.html"><em>thermo_style</em></a> command) with ID = <em>thermo_temp</em>
		and <em>thermo_press</em>. This means you can change the attributes of this
		fix’s temperature or pressure via the
		<a class="reference internal" href="compute_modify.html"><em>compute_modify</em></a> command or print this temperature
		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.
		It also means that changing attributes of <em>thermo_temp</em> or
		<em>thermo_press</em> will have no effect on this fix.</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"><em>Section_accelerate</em></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>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>-suffix command-line switch</span></a> when you invoke LAMMPS, or you can
		use the <a class="reference internal" href="suffix.html"><em>suffix</em></a> command in your input script.</p>
		<p>See <a class="reference internal" href="Section_accelerate.html"><em>Section_accelerate</em></a> of the manual for
		more instructions on how to use the accelerated styles effectively.</p>
		</div>
		<div class="section" id="restart-fix-modify-output-run-start-stop-minimize-info">
		<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>
		<p>This fix writes the state of the Nose/Hoover barostat to <a class="reference internal" href="restart.html"><em>binary restart files</em></a>. See the <a class="reference internal" href="read_restart.html"><em>read_restart</em></a>
		command for info on how to re-specify a fix in an input script that
		reads a restart file, so that the operation of the fix continues in an
		uninterrupted fashion.</p>
		<p>The <a class="reference internal" href="fix_modify.html"><em>fix_modify</em></a> <em>temp</em> and <em>press</em> options are
		supported by this fix. You can use them to assign a
		<a class="reference internal" href="compute.html"><em>compute</em></a> you have defined to this fix which will be used
		in its thermostatting or barostatting procedure. If you do this, note
		that the kinetic energy derived from the compute temperature should be
		consistent with the virial term computed using all atoms for the
		pressure. LAMMPS will warn you if you choose to compute temperature
		on a subset of atoms.</p>
		<p>The <a class="reference internal" href="fix_modify.html"><em>fix_modify</em></a> <em>energy</em> option is supported by this
		fix to add the energy change induced by Nose/Hoover barostatting to
		the system’s potential energy as part of <a class="reference internal" href="thermo_style.html"><em>thermodynamic output</em></a>.</p>
		<p>This fix computes the same global scalar and global vector of
		quantities as does the <a class="reference internal" href="fix_nh.html"><em>fix nph</em></a> command.</p>
		<p>This fix can ramp its target pressure over multiple runs, using the
		<em>start</em> and <em>stop</em> keywords of the <a class="reference internal" href="run.html"><em>run</em></a> command. See the
		<a class="reference internal" href="run.html"><em>run</em></a> command for details of how to do this.</p>
		<p>This fix is not invoked during <a class="reference internal" href="minimize.html"><em>energy minimization</em></a>.</p>
		</div>
		<div class="section" id="restrictions">
		<h2>Restrictions<a class="headerlink" href="#restrictions" title="Permalink to this headline">¶</a></h2>
		<p>This fix is part of the BODY package. It is only enabled if LAMMPS
		was built with that package. See the <a class="reference internal" href="Section_start.html#start-3"><span>Making LAMMPS</span></a> section for more info.</p>
		<p>This fix requires that atoms store torque and angular momementum and a
		quaternion as defined by the <a class="reference internal" href="atom_style.html"><em>atom_style body</em></a>
		command.</p>
		</div>
		<div class="section" id="related-commands">
		<h2>Related commands<a class="headerlink" href="#related-commands" title="Permalink to this headline">¶</a></h2>
		<p><a class="reference internal" href="fix_nh.html"><em>fix nph</em></a>, <a class="reference internal" href="fix_nve_body.html"><em>fix nve_body</em></a>, <a class="reference internal" href="fix_nvt_body.html"><em>fix nvt_body</em></a>, <a class="reference internal" href="fix_npt_body.html"><em>fix npt_body</em></a>, <a class="reference internal" href="fix_modify.html"><em>fix_modify</em></a></p>
		<p><strong>Default:</strong> none</p>
		</div>
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doc/fix_nph_body.txt

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		"LAMMPS WWW Site"_lws - "LAMMPS Documentation"_ld - "LAMMPS Commands"_lc :c

		:link(lws,http://lammps.sandia.gov)
		:link(ld,Manual.html)
		:link(lc,Section_commands.html#comm)

		:line

		fix nph/body command :h3

		[Syntax:]

		fix ID group-ID nph/body args keyword value ... :pre

		ID, group-ID are documented in "fix"_fix.html command
		nph/body = style name of this fix command
		additional barostat related keyword/value pairs from the "fix nph"_fix_nh.html command can be appended :ul

		[Examples:]

		fix 1 all nph/body iso 0.0 0.0 1000.0
		fix 2 all nph/body x 5.0 5.0 1000.0
		fix 2 all nph/body x 5.0 5.0 1000.0 drag 0.2
		fix 2 water nph/body aniso 0.0 0.0 1000.0 dilate partial :pre

		[Description:]

		Perform constant NPH integration to update position, velocity,
		orientation, and angular velocity each timestep for body
		particles in the group using a Nose/Hoover pressure
		barostat. P is pressure; H is enthalpy. This creates a system
		trajectory consistent with the isenthalpic ensemble.

		This fix differs from the "fix nph"_fix_nh.html command, which assumes
		point particles and only updates their position and velocity.

		Additional parameters affecting the barostat are specified by keywords
		and values documented with the "fix nph"_fix_nh.html command. See,
		for example, discussion of the {aniso}, and {dilate} keywords.

		The particles in the fix group are the only ones whose velocities and
		positions are updated by the velocity/position update portion of the
		NPH integration.

		Regardless of what particles are in the fix group, a global pressure is
		computed for all particles. Similarly, when the size of the simulation
		box is changed, all particles are re-scaled to new positions, unless the
		keyword {dilate} is specified with a value of {partial}, in which case
		only the particles in the fix group are re-scaled. The latter can be
		useful for leaving the coordinates of particles in a solid substrate
		unchanged and controlling the pressure of a surrounding fluid.

		:line

		This fix computes a temperature and pressure each timestep. To do
		this, the fix creates its own computes of style "temp/body" and
		"pressure", as if these commands had been issued:

		compute fix-ID_temp all temp/body
		compute fix-ID_press all pressure fix-ID_temp :pre

		See the "compute temp/body"_compute_temp_body.html and "compute
		pressure"_compute_pressure.html commands for details. Note that the
		IDs of the new computes are the fix-ID + underscore + "temp" or fix_ID
		+ underscore + "press", and the group for the new computes is "all"
		since pressure is computed for the entire system.

		Note that these are NOT the computes used by thermodynamic output (see
		the "thermo_style"_thermo_style.html command) with ID = {thermo_temp}
		and {thermo_press}. This means you can change the attributes of this
		fix's temperature or pressure via the
		"compute_modify"_compute_modify.html command or print this temperature
		or pressure during thermodynamic output via the "thermo_style
		custom"_thermo_style.html command using the appropriate compute-ID.
		It also means that changing attributes of {thermo_temp} or
		{thermo_press} will have no effect on this fix.

		:line

		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 "Section_accelerate"_Section_accelerate.html
		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 "Making
		LAMMPS"_Section_start.html#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 "-suffix command-line
		switch"_Section_start.html#start_7 when you invoke LAMMPS, or you can
		use the "suffix"_suffix.html command in your input script.

		See "Section_accelerate"_Section_accelerate.html of the manual for
		more instructions on how to use the accelerated styles effectively.

		[Restart, fix_modify, output, run start/stop, minimize info:]

		This fix writes the state of the Nose/Hoover barostat to "binary
		restart files"_restart.html. See the "read_restart"_read_restart.html
		command for info on how to re-specify a fix in an input script that
		reads a restart file, so that the operation of the fix continues in an
		uninterrupted fashion.

		The "fix_modify"_fix_modify.html {temp} and {press} options are
		supported by this fix. You can use them to assign a
		"compute"_compute.html you have defined to this fix which will be used
		in its thermostatting or barostatting procedure. If you do this, note
		that the kinetic energy derived from the compute temperature should be
		consistent with the virial term computed using all atoms for the
		pressure. LAMMPS will warn you if you choose to compute temperature
		on a subset of atoms.

		The "fix_modify"_fix_modify.html {energy} option is supported by this
		fix to add the energy change induced by Nose/Hoover barostatting to
		the system's potential energy as part of "thermodynamic
		output"_thermo_style.html.

		This fix computes the same global scalar and global vector of
		quantities as does the "fix nph"_fix_nh.html command.

		This fix can ramp its target pressure over multiple runs, using the
		{start} and {stop} keywords of the "run"_run.html command. See the
		"run"_run.html command for details of how to do this.

		This fix is not invoked during "energy minimization"_minimize.html.

		[Restrictions:]

		This fix is part of the BODY package. It is only enabled if LAMMPS
		was built with that package. See the "Making
		LAMMPS"_Section_start.html#start_3 section for more info.

		This fix requires that atoms store torque and angular momementum and a
		quaternion as defined by the "atom_style body"_atom_style.html
		command.

		[Related commands:]

		"fix nph"_fix_nh.html, "fix nve_body"_fix_nve_body.html, "fix
		nvt_body"_fix_nvt_body.html, "fix
		npt_body"_fix_npt_body.html, "fix_modify"_fix_modify.html

		[Default:] none

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doc/fix_npt_body.txt

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