(1a82fbf0) · Commits · 郑智淋 / lammps

doc/_sources/atom_style.txt

+37 −11

Original line number	Diff line number	Diff line
		@@ -10,10 +10,10 @@ Syntax

		atom_style style args

		* style = angle or atomic or body or bond or charge or dipole or electron or ellipsoid or full or line or meso or molecular or peri or smd or sphere or tri or template or hybrid
		* style = angle or atomic or body or bond or charge or dipole or dpd or electron or ellipsoid or full or line or meso or molecular or peri or smd or sphere or tri or template or hybrid
		.. parsed-literal::

		args = none for any style except body and hybrid
		args = none for any style except the following
		body args = bstyle bstyle-args
		bstyle = style of body particles
		bstyle-args = additional arguments specific to the bstyle
		@@ -48,6 +48,12 @@ used before a simulation is setup via a :doc:`read_data <read_data>`,
		:doc:`read_restart <read_restart>`, or :doc:`create_box <create_box>`
		command.

		.. note::

		Many of the atom styles discussed here are only enabled if
		LAMMPS was built with a specific package, as listed below in the
		Restrictions section.

		Once a style is assigned, it cannot be changed, so use a style general
		enough to encompass all attributes. E.g. with style bond, angular
		terms cannot be used or added later to the model. It is OK to use a
		@@ -78,6 +84,8 @@ quantities.
		+--------------+-----------------------------------------------------+--------------------------------------+
		\| dipole \| charge and dipole moment \| system with dipolar particles \|
		+--------------+-----------------------------------------------------+--------------------------------------+
		\| dpd \| internal temperature and internal energies \| DPD particles \|
		+--------------+-----------------------------------------------------+--------------------------------------+
		\| electron \| charge and spin and eradius \| electronic force field \|
		+--------------+-----------------------------------------------------+--------------------------------------+
		\| ellipsoid \| shape, quaternion, angular momentum \| aspherical particles \|
		@@ -147,6 +155,10 @@ position, which is represented by the eradius = electron size.
		For the peri style, the particles are spherical and each stores a
		per-particle mass and volume.

		The dpd style is for dissipative particle dynamics (DPD) particles
		which store the particle internal temperature (dpdTheta), internal
		conductive energy (uCond) and internal mechanical energy (uMech).

		The meso style is for smoothed particle hydrodynamics (SPH)
		particles which store a density (rho), energy (e), and heat capacity
		(cv).
		@@ -272,16 +284,30 @@ Restrictions
		This command cannot be used after the simulation box is defined by a
		:doc:`read_data <read_data>` or :doc:`create_box <create_box>` command.

		Many of the styles listed above are only enabled if LAMMPS was built
		with a specific package, as listed below. See the :ref:`Making LAMMPS <start_3>` section for more info.

		The angle, bond, full, molecular, and template styles are
		part of the MOLECULE package. The line and tri styles are part
		of the ASPHERE pacakge. The body style is part of the BODY package.
		The dipole style is part of the DIPOLE package. The peri style is
		part of the PERI package for Peridynamics. The electron style is
		part of the USER-EFF package for :doc:`electronic force fields <pair_eff>`. The meso style is part of the USER-SPH
		package for smoothed particle hydrodyanmics (SPH). See `this PDF guide <USER/sph/SPH_LAMMPS_userguide.pdf>`_ to using SPH in LAMMPS. The
		wavepacket style is part of the USER-AWPMD package for the
		:doc:`antisymmetrized wave packet MD method <pair_awpmd>`. They are
		only enabled if LAMMPS was built with that package. See the :ref:`Making LAMMPS <start_3>` section for more info.
		part of the MOLECULE package.

		The line and tri styles are part of the ASPHERE pacakge.

		The body style is part of the BODY package.

		The dipole style is part of the DIPOLE package.

		The peri style is part of the PERI package for Peridynamics.

		The electron style is part of the USER-EFF package for :doc:`electronic force fields <pair_eff>`.

		The dpd style is part of the USER-DPD package for dissipative
		particle dynamics (DPD).

		The meso style is part of the USER-SPH package for smoothed particle
		hydrodyanmics (SPH). See `this PDF guide <USER/sph/SPH_LAMMPS_userguide.pdf>`_ to using SPH in LAMMPS.

		The wavepacket style is part of the USER-AWPMD package for the
		:doc:`antisymmetrized wave packet MD method <pair_awpmd>`.

		Related commands
		""""""""""""""""

doc/_sources/read_data.txt

+22 −19

Original line number	Diff line number	Diff line
		@@ -582,6 +582,8 @@ of analysis.
		+------------+---------------------------------------------------------------------------+
		\| dipole \| atom-ID atom-type q x y z mux muy muz \|
		+------------+---------------------------------------------------------------------------+
		\| dpd \| atom-ID atom-type theta x y z \|
		+------------+---------------------------------------------------------------------------+
		\| electron \| atom-ID atom-type q spin eradius x y z \|
		+------------+---------------------------------------------------------------------------+
		\| ellipsoid \| atom-ID atom-type ellipsoidflag density x y z \|
		@@ -596,7 +598,7 @@ of analysis.
		+------------+---------------------------------------------------------------------------+
		\| peri \| atom-ID atom-type volume density x y z \|
		+------------+---------------------------------------------------------------------------+
		\| smd \| atom-ID atom-type molecule volume mass kernel_radius contact_radius x y z \|
		\| smd \| atom-ID atom-type molecule volume mass kernel-radius contact-radius x y z \|
		+------------+---------------------------------------------------------------------------+
		\| sphere \| atom-ID atom-type diameter density x y z \|
		+------------+---------------------------------------------------------------------------+
		@@ -609,33 +611,34 @@ of analysis.
		\| hybrid \| atom-ID atom-type x y z sub-style1 sub-style2 ... \|
		+------------+---------------------------------------------------------------------------+

		The keywords have these meanings:
		The per-atom values have these meanings and units, listed alphabetically:

		* atom-ID = integer ID of atom
		* molecule-ID = integer ID of molecule the atom belongs to
		* atom-type = type of atom (1-Ntype)
		* q = charge on atom (charge units)
		* diameter = diameter of spherical atom (distance units)
		* ellipsoidflag = 1 for ellipsoidal particles, 0 for point particles
		* lineflag = 1 for line segment particles, 0 for point particles
		* triangleflag = 1 for triangular particles, 0 for point particles
		* bodyflag = 1 for body particles, 0 for point particles
		* template-index = which molecule within the molecule template the atom is part of
		* template-atom = which atom within a template molecule the atom is
		* contact-radius = ??? (distance units)
		* cs_re,cs_im = real/imaginary parts of wavepacket coefficients
		* cv = heat capacity (need units) for SPH particles
		* density = density of particle (mass/distance^3 or mass/distance^2 or mass/distance units, depending on dimensionality of particle)
		* diameter = diameter of spherical atom (distance units)
		* e = energy (need units) for SPH particles
		* ellipsoidflag = 1 for ellipsoidal particles, 0 for point particles
		* eradius = electron radius (or fixed-core radius)
		* etag = integer ID of electron that each wavepacket belongs to
		* kernel-radius = ??? (distance units)
		* lineflag = 1 for line segment particles, 0 for point or spherical particles
		* mass = mass of particle (mass units)
		* volume = volume of particle (distance^3 units)
		* x,y,z = coordinates of atom
		* molecule-ID = integer ID of molecule the atom belongs to
		* mux,muy,muz = components of dipole moment of atom (dipole units)
		* q = charge on atom (charge units)
		* rho = density (need units) for SPH particles
		* e = energy (need units) for SPH particles
		* cv = heat capacity (need units) for SPH particles
		* spin = electron spin (+1/-1), 0 = nuclei, 2 = fixed-core, 3 = pseudo-cores (i.e. ECP)
		* eradius = electron radius (or fixed-core radius)
		* etag = integer ID of electron that each wavepacket belongs to
		* cs_re,cs_im = real/imaginary parts of wavepacket coefficients
		* kernel_radius = ??? (distance units)
		* contact_radius = ??? (distance units)
		* template-atom = which atom within a template molecule the atom is
		* template-index = which molecule within the molecule template the atom is part of
		* theta = internal temperature of a DPD particle
		* triangleflag = 1 for triangular particles, 0 for point or sperhical particles
		* volume = volume of Peridynamic particle (distance^3 units)
		* x,y,z = coordinates of atom (distance units)

		The units for these quantities depend on the unit style; see the
		:doc:`units <units>` command for details.

doc/_sources/set.txt

+5 −1

Original line number	Diff line number	Diff line
		@@ -13,7 +13,7 @@ Syntax
		* style = atom or type or mol or group or region
		* ID = atom ID range or type range or mol ID range or group ID or region ID
		* one or more keyword/value pairs may be appended
		* keyword = type or type/fraction or mol or x or y or z or charge or dipole or dipole/random or quat or quat/random or diameter or shape or length or tri or theta or theta/random or angmom or omega or mass or density or volume or image or bond or angle or dihedral or improper or meso/e or meso/cv or meso/rho or smd/contact/radius or smd/mass/density or i_name or d_name
		* keyword = type or type/fraction or mol or x or y or z or charge or dipole or dipole/random or quat or quat/random or diameter or shape or length or tri or theta or theta/random or angmom or omega or mass or density or volume or image or bond or angle or dihedral or improper or meso/e or meso/cv or meso/rho or smd/contact/radius or smd/mass/density or dpd/theta or i_name or d_name
		.. parsed-literal::

		type value = atom type
		@@ -83,6 +83,7 @@ Syntax
		value can be an atom-style variable (see below)
		smd/mass/density = set particle mass based on volume by providing a mass density
		value can be an atom-style variable (see below)
		dpd/theta value = internal temperature of DPD particles (temperature units)
		i_name value = value for custom integer vector with name
		d_name value = value for custom floating-point vector with name

		@@ -382,6 +383,9 @@ other. Note that the SPH smoothing kernel diameter used for computing
		long range, nonlocal interactions, is set using the diameter
		keyword.

		Keyword dpd/theta sets the internal temperature of a DPD particle
		as defined by the USER-DPD package.

		Keywords i_name and d_name refer to custom integer and
		floating-point properties that have been added to each atom via the
		:doc:`fix property/atom <fix_property_atom>` command. When that command

doc/atom_style.html

+41 −23

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

doc/compute_dpd.html

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