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This commit is contained in:
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parent
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@ -15,7 +15,7 @@
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</P>
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<PRE>atom_style style args
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</PRE>
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<UL><LI>style = <I>angle</I> or <I>atomic</I> or <I>bond</I> or <I>charge</I> or <I>colloid</I> or <I>dipole</I> or <I>dpd</I> or <I>ellipsoid</I> or <I>full</I> or <I>granular</I> or <I>molecular</I> or <I>peri</I> or <I>hybrid</I>
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<UL><LI>style = <I>angle</I> or <I>atomic</I> or <I>bond</I> or <I>charge</I> or <I>colloid</I> or <I>dipole</I> or <I>ellipsoid</I> or <I>full</I> or <I>granular</I> or <I>molecular</I> or <I>peri</I> or <I>hybrid</I>
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</UL>
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<PRE> args = none for any style except <I>hybrid</I>
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<I>hybrid</I> args = list of one or more sub-styles
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@ -59,7 +59,6 @@ quantities.
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<TR><TD ><I>charge</I> </TD><TD > charge </TD><TD > atomic system with charges </TD></TR>
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<TR><TD ><I>colloid</I> </TD><TD > angular velocity </TD><TD > extended spherical particles </TD></TR>
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<TR><TD ><I>dipole</I> </TD><TD > charge and dipole moment </TD><TD > atomic system with dipoles </TD></TR>
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<TR><TD ><I>dpd</I> </TD><TD > default values, also communicates velocities </TD><TD > DPD models </TD></TR>
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<TR><TD ><I>ellipsoid</I> </TD><TD > quaternion for particle orientation, angular momentum </TD><TD > extended aspherical particles </TD></TR>
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<TR><TD ><I>full</I> </TD><TD > molecular + charge </TD><TD > bio-molecules </TD></TR>
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<TR><TD ><I>granular</I> </TD><TD > diameter, density, angular velocity </TD><TD > granular models </TD></TR>
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@ -68,7 +67,7 @@ quantities.
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</TD></TR></TABLE></DIV>
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<P>All of the styles define point particles, except the <I>colloid</I>,
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<I>dipole</I>, <I>ellipsoid</I>, <I>granular</I>, and <I>peri</I> styles. These define
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<I>dipole</I>, <I>ellipsoid</I>, <I>granular</I>, and <I>peri</I> styles, which define
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finite-size particles. For <I>colloid</I>, <I>dipole</I>, and <I>ellipsoid</I>
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systems, the <A HREF = "shape.html">shape</A> command is used to specify the size
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and shape of particles on a per-type basis, which is spherical for
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@ -85,13 +84,6 @@ the specified diameter and density are used to calculate each
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particle's mass. For <I>peri</I> systems, the speficied volume and density
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are used to calculate each particle's mass.
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</P>
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<P>Only the <I>colloid</I>, <I>dpd</I>, and <I>granular</I> styles communicate
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velocities and angular velocities (if defined) with ghost atoms; the
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others do not. This is because the pairwise interactions calculated
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by the pair styles that typically use these atom styles
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(e.g. <A HREF = "pair_dpd.html">pair_style dpd</A> and <A HREF = "pair_gran.html">pair_style
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granular</A>) require velocities of both particles.
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</P>
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<HR>
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<P>Typically, simulations require only a single (non-hybrid) atom style.
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@ -103,10 +95,10 @@ If some atoms have bonds, but others do not, use the <I>bond</I> style.
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</P>
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<P>The only scenario where the <I>hybrid</I> style is needed is if there is no
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single style which defines all needed properties of all atoms. For
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example, if you want charged DPD particles, you would need to use
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"atom_style hybrid dpd charge". When a hybrid style is used, atoms
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store and communicate the union of all quantities implied by the
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individual styles.
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example, if you want colloidal particles with charge, you would need
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to use "atom_style hybrid colloid charge". When a hybrid style is
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used, atoms store and communicate the union of all quantities implied
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by the individual styles.
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</P>
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<P>LAMMPS can be extended with new atom styles; see <A HREF = "Section_modify.html">this
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section</A>.
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@ -118,13 +110,12 @@ section</A>.
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</P>
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<P>The <I>angle</I>, <I>bond</I>, <I>full</I>, and <I>molecular</I> styles are part of the
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"molecular" package. The <I>granular</I> style is part of the "granular"
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package. The <I>dpd</I> style is part of the "dpd" package. The <I>colloid</I>
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style is part of the "colloid" package. The <I>dipole</I> style is part of
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the "dipole" package. The <I>ellipsoid</I> style is part of the "asphere"
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package. The <I>peri</I> style is part of the "peri" package for
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Peridynamics. They are only enabled if LAMMPS was built with that
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package. See the <A HREF = "Section_start.html#2_3">Making LAMMPS</A> section for
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more info.
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package. The <I>colloid</I> style is part of the "colloid" package. The
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<I>dipole</I> style is part of the "dipole" package. The <I>ellipsoid</I> style
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is part of the "asphere" package. The <I>peri</I> style is part of the
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"peri" package for Peridynamics. They are only enabled if LAMMPS was
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built with that package. See the <A HREF = "Section_start.html#2_3">Making
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LAMMPS</A> section for more info.
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</P>
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<P><B>Related commands:</B>
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</P>
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@ -13,7 +13,7 @@ atom_style command :h3
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atom_style style args :pre
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style = {angle} or {atomic} or {bond} or {charge} or {colloid} or {dipole} or \
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{dpd} or {ellipsoid} or {full} or {granular} or {molecular} or \
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{ellipsoid} or {full} or {granular} or {molecular} or \
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{peri} or {hybrid} :ul
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args = none for any style except {hybrid}
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{hybrid} args = list of one or more sub-styles :pre
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@ -56,7 +56,6 @@ quantities.
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{charge} | charge | atomic system with charges |
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{colloid} | angular velocity | extended spherical particles |
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{dipole} | charge and dipole moment | atomic system with dipoles |
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{dpd} | default values, also communicates velocities | DPD models |
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{ellipsoid} | quaternion for particle orientation, angular momentum | extended aspherical particles |
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{full} | molecular + charge | bio-molecules |
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{granular} | diameter, density, angular velocity | granular models |
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@ -64,7 +63,7 @@ quantities.
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{peri} | density, volume | mesocopic Peridynamic models :tb(c=3,s=|)
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All of the styles define point particles, except the {colloid},
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{dipole}, {ellipsoid}, {granular}, and {peri} styles. These define
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{dipole}, {ellipsoid}, {granular}, and {peri} styles, which define
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finite-size particles. For {colloid}, {dipole}, and {ellipsoid}
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systems, the "shape"_shape.html command is used to specify the size
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and shape of particles on a per-type basis, which is spherical for
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@ -81,13 +80,6 @@ the specified diameter and density are used to calculate each
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particle's mass. For {peri} systems, the speficied volume and density
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are used to calculate each particle's mass.
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Only the {colloid}, {dpd}, and {granular} styles communicate
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velocities and angular velocities (if defined) with ghost atoms; the
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others do not. This is because the pairwise interactions calculated
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by the pair styles that typically use these atom styles
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(e.g. "pair_style dpd"_pair_dpd.html and "pair_style
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granular"_pair_gran.html) require velocities of both particles.
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:line
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Typically, simulations require only a single (non-hybrid) atom style.
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@ -99,10 +91,10 @@ If some atoms have bonds, but others do not, use the {bond} style.
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The only scenario where the {hybrid} style is needed is if there is no
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single style which defines all needed properties of all atoms. For
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example, if you want charged DPD particles, you would need to use
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"atom_style hybrid dpd charge". When a hybrid style is used, atoms
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store and communicate the union of all quantities implied by the
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individual styles.
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example, if you want colloidal particles with charge, you would need
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to use "atom_style hybrid colloid charge". When a hybrid style is
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used, atoms store and communicate the union of all quantities implied
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by the individual styles.
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LAMMPS can be extended with new atom styles; see "this
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section"_Section_modify.html.
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@ -114,13 +106,12 @@ This command cannot be used after the simulation box is defined by a
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The {angle}, {bond}, {full}, and {molecular} styles are part of the
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"molecular" package. The {granular} style is part of the "granular"
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package. The {dpd} style is part of the "dpd" package. The {colloid}
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style is part of the "colloid" package. The {dipole} style is part of
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the "dipole" package. The {ellipsoid} style is part of the "asphere"
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package. The {peri} style is part of the "peri" package for
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Peridynamics. They are only enabled if LAMMPS was built with that
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package. See the "Making LAMMPS"_Section_start.html#2_3 section for
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more info.
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package. The {colloid} style is part of the "colloid" package. The
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{dipole} style is part of the "dipole" package. The {ellipsoid} style
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is part of the "asphere" package. The {peri} style is part of the
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"peri" package for Peridynamics. They are only enabled if LAMMPS was
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built with that package. See the "Making
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LAMMPS"_Section_start.html#2_3 section for more info.
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[Related commands:]
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@ -19,10 +19,11 @@
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<LI>zero or more keyword/value pairs may be appended
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<LI>keyword = <I>group</I> or <I>cutoff</I>
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<LI>keyword = <I>cutoff</I> or <I>group</I> or <I>vel</I>
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<PRE> <I>group</I> value = group-ID = only communicate atoms in the group
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<I>cutoff</I> value = Rcut (distance units) = communicate atoms from this far away
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<PRE> <I>cutoff</I> value = Rcut (distance units) = communicate atoms from this far away
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<I>group</I> value = group-ID = only communicate atoms in the group
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<I>vel</I> value = <I>yes</I> or <I>no</I> = do or do not communicate velocity info with ghost atoms
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</PRE>
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</UL>
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@ -30,7 +31,8 @@
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</P>
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<PRE>communicate multi
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communicate multi group solvent
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communicate single cutoff 5.0
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communicate single ghost yes
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communicate single cutoff 5.0 ghost yes
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</PRE>
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<P><B>Description:</B>
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</P>
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@ -52,13 +54,6 @@ communicated. See the <A HREF = "neighbor.html">neighbor multi</A> command for
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neighbor list construction option that may also be beneficial for
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simulations of this kind.
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</P>
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<P>The <I>group</I> option will limit communication to atoms in the specified
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group. This can be useful for models where no ghost atoms are needed
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for some kinds of particles. All atoms (not just those in the
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specified group) will still migrate to new processors as they move.
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The group specified with this option must also be specified via the
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<A HREF = "atom_modify.html">atom_modify first</A> command.
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</P>
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<P>The <I>cutoff</I> option allows you to set a ghost cutoff distance, which
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is the distance from the borders of a processor's sub-domain at which
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ghost atoms are acquired from other processors. By default the ghost
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@ -98,6 +93,22 @@ performs (e.g. locate neighbors of ghost atoms in a multibody pair
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potential). Setting the ghost cutoff appropriately can insure it will
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find the needed atoms.
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</P>
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<P>The <I>group</I> option will limit communication to atoms in the specified
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group. This can be useful for models where no ghost atoms are needed
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for some kinds of particles. All atoms (not just those in the
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specified group) will still migrate to new processors as they move.
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The group specified with this option must also be specified via the
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<A HREF = "atom_modify.html">atom_modify first</A> command.
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</P>
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<P>The <I>vel</I> option enables velocity information to be communicated with
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ghost particles. Depending on the <A HREF = "atom_style.html">atom_style</A>,
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velocity info includes the translational velocity, angular velocity,
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and angular momentum of a particle. If the <I>vel</I> option is set to
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<I>yes</I>, then ghost atoms store these quantities; if <I>no</I> then they do
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not. The <I>yes</I> setting is needed by some pair styles which require
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the velocity state of both the I and J particles to compute a pairwise
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I,J interaction.
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</P>
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<P><B>Restrictions:</B> none
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</P>
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<P><B>Related commands:</B>
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@ -106,8 +117,8 @@ find the needed atoms.
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</P>
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<P><B>Default:</B>
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</P>
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<P>The default settings are style = single, group = all, cutoff = 0.0.
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The cutoff default of 0.0 means that effectively ghost cutoff =
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<P>The default settings are style = single, group = all, cutoff = 0.0,
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ghost = no. The cutoff default of 0.0 means that ghost cutoff =
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neighbor cutoff = pairwise force cutoff + neighbor skin.
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</P>
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</HTML>
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@ -14,16 +14,18 @@ communicate style keyword value ... :pre
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style = {single} or {multi} :ulb,l
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zero or more keyword/value pairs may be appended :l
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keyword = {group} or {cutoff} :l
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keyword = {cutoff} or {group} or {vel} :l
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{cutoff} value = Rcut (distance units) = communicate atoms from this far away
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{group} value = group-ID = only communicate atoms in the group
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{cutoff} value = Rcut (distance units) = communicate atoms from this far away :pre
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{vel} value = {yes} or {no} = do or do not communicate velocity info with ghost atoms :pre
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:ule
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[Examples:]
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communicate multi
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communicate multi group solvent
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communicate single cutoff 5.0 :pre
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communicate single ghost yes
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communicate single cutoff 5.0 ghost yes :pre
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[Description:]
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@ -45,13 +47,6 @@ communicated. See the "neighbor multi"_neighbor.html command for a
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neighbor list construction option that may also be beneficial for
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simulations of this kind.
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The {group} option will limit communication to atoms in the specified
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group. This can be useful for models where no ghost atoms are needed
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for some kinds of particles. All atoms (not just those in the
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specified group) will still migrate to new processors as they move.
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The group specified with this option must also be specified via the
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"atom_modify first"_atom_modify.html command.
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The {cutoff} option allows you to set a ghost cutoff distance, which
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is the distance from the borders of a processor's sub-domain at which
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ghost atoms are acquired from other processors. By default the ghost
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@ -91,6 +86,22 @@ performs (e.g. locate neighbors of ghost atoms in a multibody pair
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potential). Setting the ghost cutoff appropriately can insure it will
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find the needed atoms.
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The {group} option will limit communication to atoms in the specified
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group. This can be useful for models where no ghost atoms are needed
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for some kinds of particles. All atoms (not just those in the
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specified group) will still migrate to new processors as they move.
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The group specified with this option must also be specified via the
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"atom_modify first"_atom_modify.html command.
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The {vel} option enables velocity information to be communicated with
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ghost particles. Depending on the "atom_style"_atom_style.html,
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velocity info includes the translational velocity, angular velocity,
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and angular momentum of a particle. If the {vel} option is set to
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{yes}, then ghost atoms store these quantities; if {no} then they do
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not. The {yes} setting is needed by some pair styles which require
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the velocity state of both the I and J particles to compute a pairwise
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I,J interaction.
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[Restrictions:] none
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[Related commands:]
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@ -99,6 +110,6 @@ find the needed atoms.
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[Default:]
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The default settings are style = single, group = all, cutoff = 0.0.
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The cutoff default of 0.0 means that effectively ghost cutoff =
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The default settings are style = single, group = all, cutoff = 0.0,
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ghost = no. The cutoff default of 0.0 means that ghost cutoff =
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neighbor cutoff = pairwise force cutoff + neighbor skin.
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|
|
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@ -272,7 +272,6 @@ of analysis.
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<TR><TD >charge</TD><TD > atom-ID atom-type q x y z</TD></TR>
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<TR><TD >colloid</TD><TD > atom-ID atom-type x y z</TD></TR>
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<TR><TD >dipole</TD><TD > atom-ID atom-type q x y z mux muy muz</TD></TR>
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<TR><TD >dpd</TD><TD > atom-ID atom-type x y z</TD></TR>
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<TR><TD >ellipsoid</TD><TD > atom-ID atom-type x y z quatw quati quatj quatk</TD></TR>
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<TR><TD >full</TD><TD > atom-ID molecule-ID atom-type q x y z</TD></TR>
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<TR><TD >granular</TD><TD > atom-ID atom-type diameter density x y z</TD></TR>
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@ -252,7 +252,6 @@ bond: atom-ID molecule-ID atom-type x y z
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charge: atom-ID atom-type q x y z
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colloid: atom-ID atom-type x y z
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dipole: atom-ID atom-type q x y z mux muy muz
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dpd: atom-ID atom-type x y z
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ellipsoid: atom-ID atom-type x y z quatw quati quatj quatk
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full: atom-ID molecule-ID atom-type q x y z
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granular: atom-ID atom-type diameter density x y z
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Reference in New Issue