forked from lijiext/lammps
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This commit is contained in:
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parent
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@ -15,13 +15,15 @@
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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>body</I> or <I>bond</I> or <I>charge</I> or <I>dipole</I> or <I>electron</I> or <I>ellipsoid</I> or <I>full</I> or <I>line</I> or <I>meso</I> or <I>molecular</I> or <I>peri</I> or <I>sphere</I> or <I>tri</I> or <I>hybrid</I>
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<UL><LI>style = <I>angle</I> or <I>atomic</I> or <I>body</I> or <I>bond</I> or <I>charge</I> or <I>dipole</I> or <I>electron</I> or <I>ellipsoid</I> or <I>full</I> or <I>line</I> or <I>meso</I> or <I>molecular</I> or <I>peri</I> or <I>sphere</I> or <I>tri</I> or <I>template</I> or <I>hybrid</I>
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</UL>
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<PRE> args = none for any style except <I>body</I> and <I>hybrid</I>
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<I>body</I> args = bstyle bstyle-args
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bstyle = style of body particles
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bstyle-args = additional arguments specific to the bstyle
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see the <A HREF = "body.html">body</A> doc page for details
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<I>template</I> args = template-ID
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template-ID = ID of molecule template specified in a separate <A HREF = "molecule.html">molecule</A> command
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<I>hybrid</I> args = list of one or more sub-styles, each with their args
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</PRE>
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<P><B>Examples:</B>
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@ -31,7 +33,8 @@ atom_style bond
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atom_style full
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atom_style body nparticle 2 10
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atom_style hybrid charge bond
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atom_style hybrid charge body nparticle 2 5
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atom_style hybrid charge body nparticle 2 5
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atom_style template myMols
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</PRE>
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<P><B>Description:</B>
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</P>
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@ -73,6 +76,7 @@ quantities.
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<TR><TD ><I>molecular</I> </TD><TD > bonds, angles, dihedrals, impropers </TD><TD > uncharged molecules </TD></TR>
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<TR><TD ><I>peri</I> </TD><TD > mass, volume </TD><TD > mesocopic Peridynamic models </TD></TR>
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<TR><TD ><I>sphere</I> </TD><TD > diameter, mass, angular velocity </TD><TD > granular models </TD></TR>
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<TR><TD ><I>template</I> </TD><TD > template index, template atom </TD><TD > small molecules with fixed topology </TD></TR>
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<TR><TD ><I>tri</I> </TD><TD > corner points, angular momentum </TD><TD > rigid bodies </TD></TR>
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<TR><TD ><I>wavepacket</I> </TD><TD > charge, spin, eradius, etag, cs_re, cs_im </TD><TD > AWPMD
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</TD></TR></TABLE></DIV>
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@ -92,9 +96,9 @@ output the custom values.
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14</A> for an overview of using finite-size
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particle models with LAMMPS.
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</P>
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<P>All of the styles assign mass to particles on a per-type basis, using
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the <A HREF = "mass.html">mass</A> command, except for the finite-size particle
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styles. They assign mass to individual particles on a per-particle
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<P>All of the point-particle styles assign mass to particles on a
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per-type basis, using the <A HREF = "mass.html">mass</A> command, The finite-size
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particle styles assign mass to individual particles on a per-particle
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basis.
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</P>
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<P>For the <I>sphere</I> style, the particles are spheres and each stores a
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@ -133,6 +137,16 @@ end points of the line segment).
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stores a per-particle mass and size and orientation (i.e. the corner
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points of the triangle).
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</P>
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<P>The <I>template</I> style allows molecular topolgy (bonds,angles,etc) to be
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defined via a molecule template using the <A HREF = "molecule.txt">molecule</A>
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command. The template stores one or more molecules with a single copy
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of the topology info (bonds,angles,etc) of each. Individual atoms
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only store a template index and template atom to identify which
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molecule and which atom-within-the-molecule they represent. Using the
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<I>template</I> style instead of the <I>bond</I>, <I>angle</I>, <I>molecular</I> styles
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can save memory for systems comprised of a large number of small
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molecules, all of a single type (or small number of types).
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</P>
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<P>For the <I>body</I> style, the particles are arbitrary bodies with internal
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attributes defined by the "style" of the bodies, which is specified by
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the <I>bstyle</I> argument. Body particles can represent complex entities,
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@ -165,6 +179,10 @@ torque, you would need to use "atom_style hybrid sphere dipole". When
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a hybrid style is used, atoms store and communicate the union of all
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quantities implied by the individual styles.
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</P>
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<P>When using the <I>hybrid</I> style, you cannot combine the <I>template</I> style
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with another molecular style that stores bond,angle,etc info on a
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per-atom basis.
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</P>
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<P>LAMMPS can be extended with new atom styles as well as new body
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styles; see <A HREF = "Section_modify.html">this section</A>.
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</P>
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@ -173,10 +191,10 @@ styles; see <A HREF = "Section_modify.html">this section</A>.
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<P>This command cannot be used after the simulation box is defined by a
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<A HREF = "read_data.html">read_data</A> or <A HREF = "create_box.html">create_box</A> command.
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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>line</I> and <I>tri</I> styles are part of the
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ASPHERE pacakge. The <I>body</I> style is part of the BODY package. The
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<I>dipole</I> style is part of the DIPOLE package. The <I>peri</I> style is
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<P>The <I>angle</I>, <I>bond</I>, <I>full</I>, <I>molecular</I>, and <I>template</I> styles are
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part of the MOLECULAR package. The <I>line</I> and <I>tri</I> styles are part
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of the ASPHERE pacakge. The <I>body</I> style is part of the BODY package.
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The <I>dipole</I> style is part of the DIPOLE package. The <I>peri</I> style is
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part of the PERI package for Peridynamics. The <I>electron</I> style is
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part of the USER-EFF package for <A HREF = "pair_eff.html">electronic force
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fields</A>. The <I>meso</I> style is part of the USER-SPH
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@ -14,12 +14,14 @@ atom_style style args :pre
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style = {angle} or {atomic} or {body} or {bond} or {charge} or {dipole} or \
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{electron} or {ellipsoid} or {full} or {line} or {meso} or \
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{molecular} or {peri} or {sphere} or {tri} or {hybrid} :ul
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{molecular} or {peri} or {sphere} or {tri} or {template} or {hybrid} :ul
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args = none for any style except {body} and {hybrid}
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{body} args = bstyle bstyle-args
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bstyle = style of body particles
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bstyle-args = additional arguments specific to the bstyle
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see the "body"_body.html doc page for details
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{template} args = template-ID
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template-ID = ID of molecule template specified in a separate "molecule"_molecule.html command
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{hybrid} args = list of one or more sub-styles, each with their args :pre
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[Examples:]
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atom_style full
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atom_style body nparticle 2 10
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atom_style hybrid charge bond
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atom_style hybrid charge body nparticle 2 5 :pre
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atom_style hybrid charge body nparticle 2 5
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atom_style template myMols :pre
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[Description:]
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@ -70,6 +73,7 @@ quantities.
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{molecular} | bonds, angles, dihedrals, impropers | uncharged molecules |
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{peri} | mass, volume | mesocopic Peridynamic models |
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{sphere} | diameter, mass, angular velocity | granular models |
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{template} | template index, template atom | small molecules with fixed topology |
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{tri} | corner points, angular momentum | rigid bodies |
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{wavepacket} | charge, spin, eradius, etag, cs_re, cs_im | AWPMD :tb(c=3,s=|)
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@ -88,9 +92,9 @@ All of the above styles define point particles, except the {sphere},
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14"_Section_howto.html#howto_14 for an overview of using finite-size
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particle models with LAMMPS.
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All of the styles assign mass to particles on a per-type basis, using
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the "mass"_mass.html command, except for the finite-size particle
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styles. They assign mass to individual particles on a per-particle
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All of the point-particle styles assign mass to particles on a
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per-type basis, using the "mass"_mass.html command, The finite-size
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particle styles assign mass to individual particles on a per-particle
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basis.
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For the {sphere} style, the particles are spheres and each stores a
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@ -129,6 +133,16 @@ For the {tri} style, the particles are planar triangles and each
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stores a per-particle mass and size and orientation (i.e. the corner
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points of the triangle).
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The {template} style allows molecular topolgy (bonds,angles,etc) to be
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defined via a molecule template using the "molecule"_molecule.txt
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command. The template stores one or more molecules with a single copy
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of the topology info (bonds,angles,etc) of each. Individual atoms
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only store a template index and template atom to identify which
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molecule and which atom-within-the-molecule they represent. Using the
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{template} style instead of the {bond}, {angle}, {molecular} styles
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can save memory for systems comprised of a large number of small
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molecules, all of a single type (or small number of types).
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For the {body} style, the particles are arbitrary bodies with internal
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attributes defined by the "style" of the bodies, which is specified by
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the {bstyle} argument. Body particles can represent complex entities,
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@ -161,6 +175,10 @@ torque, you would need to use "atom_style hybrid sphere dipole". When
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a hybrid style is used, atoms store and communicate the union of all
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quantities implied by the individual styles.
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When using the {hybrid} style, you cannot combine the {template} style
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with another molecular style that stores bond,angle,etc info on a
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per-atom basis.
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LAMMPS can be extended with new atom styles as well as new body
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styles; see "this section"_Section_modify.html.
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@ -169,10 +187,10 @@ styles; see "this section"_Section_modify.html.
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This command cannot be used after the simulation box is defined by a
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"read_data"_read_data.html or "create_box"_create_box.html command.
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The {angle}, {bond}, {full}, and {molecular} styles are part of the
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MOLECULAR package. The {line} and {tri} styles are part of the
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ASPHERE pacakge. The {body} style is part of the BODY package. The
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{dipole} style is part of the DIPOLE package. The {peri} style is
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The {angle}, {bond}, {full}, {molecular}, and {template} styles are
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part of the MOLECULAR package. The {line} and {tri} styles are part
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of the ASPHERE pacakge. The {body} style is part of the BODY package.
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The {dipole} style is part of the DIPOLE package. The {peri} style is
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part of the PERI package for Peridynamics. The {electron} style is
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part of the USER-EFF package for "electronic force
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fields"_pair_eff.html. The {meso} style is part of the USER-SPH
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@ -343,6 +343,7 @@ of analysis.
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<TR><TD >molecular</TD><TD > atom-ID molecule-ID atom-type x y z</TD></TR>
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<TR><TD >peri</TD><TD > atom-ID atom-type volume density x y z</TD></TR>
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<TR><TD >sphere</TD><TD > atom-ID atom-type diameter density x y z</TD></TR>
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<TR><TD >template</TD><TD > atom-ID molecule-ID template-index template-atom atom-type x y z</TD></TR>
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<TR><TD >tri</TD><TD > atom-ID molecule-ID atom-type triangleflag density x y z</TD></TR>
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<TR><TD >wavepacket</TD><TD > atom-ID atom-type charge spin eradius etag cs_re cs_im x y z</TD></TR>
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<TR><TD >hybrid</TD><TD > atom-ID atom-type x y z sub-style1 sub-style2 ...
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@ -359,6 +360,8 @@ of analysis.
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<LI>lineflag = 1 for line segment particles, 0 for point particles
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<LI>triangleflag = 1 for triangular particles, 0 for point particles
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<LI>bodyflag = 1 for body particles, 0 for point particles
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<LI>template-index = which molecule within the molecule template the atom is part of
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<LI>template-atom = which atom within a template molecule the atom is
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<LI>density = density of particle (mass/distance^3 or mass/distance^2 or mass/distance units, depending on dimensionality of particle)
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<LI>mass = mass of particle (mass units)
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<LI>volume = volume of particle (distance^3 units)
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@ -382,11 +385,11 @@ setting in the data file header.
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in dump files. Normally, it is a unique value from 1 to Natoms for
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each atom. Unique values larger than Natoms can be used, but they
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will cause extra memory to be allocated on each processor, if an atom
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map array is used (see the <A HREF = "atom_modify.html">atom_modify</A> command).
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If an atom map array is not used (e.g. an atomic system with no
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bonds), and velocities are not assigned in the data file, and you
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don't care if unique atom IDs appear in dump files, then the atom-IDs
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can all be set to 0.
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map array is used, but not if an atom map hash is used; see the
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<A HREF = "atom_modify.html">atom_modify</A> command for details. If an atom map is
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not used (e.g. an atomic system with no bonds), and you don't care if
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unique atom IDs appear in dump files, then the atom-IDs can all be set
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to 0.
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</P>
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<P>The molecule ID is a 2nd identifier attached to an atom. Normally, it
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is a number from 1 to N, identifying which molecule the atom belongs
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@ -403,6 +406,16 @@ Additional attributes must be defined for each ellipsoid, line,
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triangle, or body in the corresponding <I>Ellipsoids</I>, <I>Lines</I>,
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<I>Triangles</I>, or <I>Bodies</I> section.
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</P>
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<P>The <I>template-index</I> and <I>template-atom</I> are only defined used by
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<A HREF = "atom_style.html">atom_style template</A>. In this case the
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<A HREF = "molecule.html">molecule</A> command is used to define a molecule template
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which contains one or more molecules. If an atom belongs to one of
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those molecules, its <I>template-index</I> and <I>template-atom</I> are both set
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to positive integers; if not the values are both 0. The
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<I>template-index</I> is which molecule (1 to Nmols) the atom belongs to.
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The <I>template-atom</I> is which atom (1 to Natoms) within the molecule
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the atom is.
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</P>
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<P>Some pair styles and fixes and computes that operate on finite-size
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particles allow for a mixture of finite-size and point particles. See
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the doc pages of individual commands for details.
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|
|
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@ -320,6 +320,7 @@ meso: atom-ID atom-type rho e cv x y z
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molecular: atom-ID molecule-ID atom-type x y z
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peri: atom-ID atom-type volume density x y z
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sphere: atom-ID atom-type diameter density x y z
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template: atom-ID molecule-ID template-index template-atom atom-type x y z
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tri: atom-ID molecule-ID atom-type triangleflag density x y z
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wavepacket: atom-ID atom-type charge spin eradius etag cs_re cs_im x y z
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hybrid: atom-ID atom-type x y z sub-style1 sub-style2 ... :tb(s=:)
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@ -335,6 +336,8 @@ ellipsoidflag = 1 for ellipsoidal particles, 0 for point particles
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lineflag = 1 for line segment particles, 0 for point particles
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triangleflag = 1 for triangular particles, 0 for point particles
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bodyflag = 1 for body particles, 0 for point particles
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template-index = which molecule within the molecule template the atom is part of
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template-atom = which atom within a template molecule the atom is
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density = density of particle (mass/distance^3 or mass/distance^2 or mass/distance units, depending on dimensionality of particle)
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mass = mass of particle (mass units)
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volume = volume of particle (distance^3 units)
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@ -358,11 +361,11 @@ The atom-ID is used to identify the atom throughout the simulation and
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in dump files. Normally, it is a unique value from 1 to Natoms for
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each atom. Unique values larger than Natoms can be used, but they
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will cause extra memory to be allocated on each processor, if an atom
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map array is used (see the "atom_modify"_atom_modify.html command).
|
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If an atom map array is not used (e.g. an atomic system with no
|
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bonds), and velocities are not assigned in the data file, and you
|
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don't care if unique atom IDs appear in dump files, then the atom-IDs
|
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can all be set to 0.
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map array is used, but not if an atom map hash is used; see the
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"atom_modify"_atom_modify.html command for details. If an atom map is
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not used (e.g. an atomic system with no bonds), and you don't care if
|
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unique atom IDs appear in dump files, then the atom-IDs can all be set
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to 0.
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|
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The molecule ID is a 2nd identifier attached to an atom. Normally, it
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is a number from 1 to N, identifying which molecule the atom belongs
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|
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@ -379,6 +382,16 @@ Additional attributes must be defined for each ellipsoid, line,
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triangle, or body in the corresponding {Ellipsoids}, {Lines},
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{Triangles}, or {Bodies} section.
|
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|
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The {template-index} and {template-atom} are only defined used by
|
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"atom_style template"_atom_style.html. In this case the
|
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"molecule"_molecule.html command is used to define a molecule template
|
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which contains one or more molecules. If an atom belongs to one of
|
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those molecules, its {template-index} and {template-atom} are both set
|
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to positive integers; if not the values are both 0. The
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{template-index} is which molecule (1 to Nmols) the atom belongs to.
|
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The {template-atom} is which atom (1 to Natoms) within the molecule
|
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the atom is.
|
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|
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Some pair styles and fixes and computes that operate on finite-size
|
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particles allow for a mixture of finite-size and point particles. See
|
||||
the doc pages of individual commands for details.
|
||||
|
|
|
|||
Loading…
Reference in New Issue