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\documentclass[12pt,article]{article}
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\usepackage{indentfirst}
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\usepackage{amsmath}
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\begin{document}
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\begin{eqnarray*}
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r_{c}^{fcc} & = & \frac{1}{2} \left(\frac{\sqrt{2}}{2} + 1\right) \mathrm{a} \simeq 0.8536 \:\mathrm{a} \\
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r_{c}^{bcc} & = & \frac{1}{2}(\sqrt{2} + 1) \mathrm{a} \simeq 1.207 \:\mathrm{a} \\
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r_{c}^{hcp} & = & \frac{1}{2}\left(1+\sqrt{\frac{4+2x^{2}}{3}}\right) \mathrm{a}
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\end{eqnarray*}
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\end{document}
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\documentclass[12pt,article]{article}
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\usepackage{indentfirst}
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\usepackage{amsmath}
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\begin{document}
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$$
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Rc + Rs > 2*{\rm cutoff}
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$$
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\end{document}
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@ -45,28 +45,32 @@ what quantities are communicated between processors to enable forces
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to be computed, and what quantities are listed in the data file read
|
||||
by the <A HREF = "read_data.html">read_data</A> command.
|
||||
</P>
|
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<P>These are the attributes of each style. All styles store coordinates,
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velocities, atom IDs and types.
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||||
<P>These are the additional attributes of each style and the typical
|
||||
kinds of physical systems they are used to model. All styles store
|
||||
coordinates, velocities, atom IDs and types. See the
|
||||
<A HREF = "read_data.html">read_data</A>, <A HREF = "create_atoms.html">create_atoms</A>, and
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<A HREF = "set.html">set</A> commands for info on how to set these various
|
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quantities.
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</P>
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<UL><LI><I>angle</I> = bonds and angles - e.g. bead-spring polymers with stiffness
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<LI><I>atomic</I> = only the default values
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<LI><I>bond</I> = bonds - e.g. bead-spring polymers
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<LI><I>charge</I> = charge
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<LI><I>dipole</I> = charge and dipole moment
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<LI><I>dpd</I> = default values, also communicates velocities
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<LI><I>ellipsoid</I> = quaternion for particle orientation, angular velocity/momentum
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<LI><I>full</I> = molecular + charge - e.g. biomolecules, charged polymers
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<LI><I>granular</I> = granular atoms with rotational properties
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<LI><I>molecular</I> = bonds, angles, dihedrals, impropers - e.g. all-atom polymers
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<LI><I>peri</I> = mass, volume - e.g. mesocopic Peridynamics
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</UL>
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<DIV ALIGN=center><TABLE BORDER=1 >
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<TR><TD ><I>angle</I> </TD><TD > bonds and angles </TD><TD > bead-spring polymers with stiffness<I>atomic</I> </TD></TR>
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<TR><TD > only the default values </TD><TD > coarse-grain liquids, solids, metals<I>bond</I> </TD><TD > bonds </TD></TR>
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<TR><TD > bead-spring polymers<I>charge</I> </TD><TD > charge </TD><TD > atomic system with charges<I>dipole</I> </TD></TR>
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<TR><TD > charge and dipole moment </TD><TD > atomic system with dipoles<I>dpd</I> </TD><TD > default values, also communicates velocities </TD></TR>
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<TR><TD > DPD models<I>ellipsoid</I> </TD><TD > quaternion for particle orientation, angular momentum </TD><TD > aspherical particles<I>full</I> </TD></TR>
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<TR><TD > molecular + charge </TD><TD > bio-molecules<I>granular</I> </TD><TD > diameter, density, angular velocity </TD></TR>
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<TR><TD > granular models<I>molecular</I> </TD><TD > bonds, angles, dihedrals, impropers </TD><TD > uncharged molecules<I>peri</I> </TD></TR>
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<TR><TD > density, volume - mesocopic Peridynamic models
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</TD></TR></TABLE></DIV>
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|
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<P>Typically, simulations require only a single (non-hybrid) atom style.
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If some atoms in the simulation do not have all the properties defined
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by a particular style, use the simplest style that defines all the
|
||||
needed properties by any atom. For example, if some atoms in a
|
||||
simulation are charged, but others are not, use the <I>charge</I> style.
|
||||
If some atoms have bonds, but others do not, use the <I>bond</I> style.
|
||||
The only scenario where the <I>hybrid</I> style is needed is if there is no
|
||||
</P>
|
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<P>The only scenario where the <I>hybrid</I> style is needed is if there is no
|
||||
single style which defines all needed properties of all atoms.
|
||||
E.g. 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
|
||||
|
|
|
|||
|
|
@ -43,20 +43,24 @@ what quantities are communicated between processors to enable forces
|
|||
to be computed, and what quantities are listed in the data file read
|
||||
by the "read_data"_read_data.html command.
|
||||
|
||||
These are the attributes of each style. All styles store coordinates,
|
||||
velocities, atom IDs and types.
|
||||
These are the additional attributes of each style and the typical
|
||||
kinds of physical systems they are used to model. All styles store
|
||||
coordinates, velocities, atom IDs and types. See the
|
||||
"read_data"_read_data.html, "create_atoms"_create_atoms.html, and
|
||||
"set"_set.html commands for info on how to set these various
|
||||
quantities.
|
||||
|
||||
{angle} = bonds and angles - e.g. bead-spring polymers with stiffness
|
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{atomic} = only the default values
|
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{bond} = bonds - e.g. bead-spring polymers
|
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{charge} = charge
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{dipole} = charge and dipole moment
|
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{dpd} = default values, also communicates velocities
|
||||
{ellipsoid} = quaternion for particle orientation, angular velocity/momentum
|
||||
{full} = molecular + charge - e.g. biomolecules, charged polymers
|
||||
{granular} = granular atoms with rotational properties
|
||||
{molecular} = bonds, angles, dihedrals, impropers - e.g. all-atom polymers
|
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{peri} = mass, volume - e.g. mesocopic Peridynamics :ul
|
||||
{angle} : bonds and angles : bead-spring polymers with stiffness
|
||||
{atomic} : only the default values : coarse-grain liquids, solids, metals
|
||||
{bond} : bonds : bead-spring polymers
|
||||
{charge} : charge : atomic system with charges
|
||||
{dipole} : charge and dipole moment : atomic system with dipoles
|
||||
{dpd} : default values, also communicates velocities : DPD models
|
||||
{ellipsoid} : quaternion for particle orientation, angular momentum : aspherical particles
|
||||
{full} : molecular + charge : bio-molecules
|
||||
{granular} : diameter, density, angular velocity : granular models
|
||||
{molecular} : bonds, angles, dihedrals, impropers : uncharged molecules
|
||||
{peri} : density, volume - mesocopic Peridynamic models :tb(c=3,s=:)
|
||||
|
||||
Typically, simulations require only a single (non-hybrid) atom style.
|
||||
If some atoms in the simulation do not have all the properties defined
|
||||
|
|
@ -64,6 +68,7 @@ by a particular style, use the simplest style that defines all the
|
|||
needed properties by any atom. For example, if some atoms in a
|
||||
simulation are charged, but others are not, use the {charge} style.
|
||||
If some atoms have bonds, but others do not, use the {bond} style.
|
||||
|
||||
The only scenario where the {hybrid} style is needed is if there is no
|
||||
single style which defines all needed properties of all atoms.
|
||||
E.g. if you want charged DPD particles, you would need to use
|
||||
|
|
|
|||
|
|
@ -25,7 +25,7 @@
|
|||
<P><B>Description:</B>
|
||||
</P>
|
||||
<P>Define a computation that calculates the centro-symmetry parameter for
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||||
each atom in a group. In solid-state systems the centro-symmetry
|
||||
each atom in the group. In solid-state systems the centro-symmetry
|
||||
parameter is a useful measure of the local lattice disorder around an
|
||||
atom and can be used to characterize whether the atom is part of a
|
||||
perfect lattice, a local defect (e.g. a dislocation or stacking
|
||||
|
|
@ -45,9 +45,9 @@ nearest neighbors. Atoms not in the group are included in the 12
|
|||
neighbors used in this calculation.
|
||||
</P>
|
||||
<P>The neighbor list needed to compute this quantity is constructed each
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||||
time the calculation is performed (i.e. each time a snapshot of atoms
|
||||
time the calculation is performed (e.g. each time a snapshot of atoms
|
||||
is dumped). Thus it can be inefficient to compute/dump this quantity
|
||||
too frequently or to have multiple compute/dump commands, each of a
|
||||
too frequently or to have multiple compute/dump commands, each with a
|
||||
<I>centro/atom</I> style.
|
||||
</P>
|
||||
<P><B>Output info:</B>
|
||||
|
|
@ -59,7 +59,9 @@ output options.
|
|||
</P>
|
||||
<P><B>Restrictions:</B> none
|
||||
</P>
|
||||
<P><B>Related commands:</B> none
|
||||
<P><B>Related commands:</B>
|
||||
</P>
|
||||
<P><A HREF = "compute_cna_atom.html">compute cna/atom</A>
|
||||
</P>
|
||||
<P><B>Default:</B> none
|
||||
</P>
|
||||
|
|
|
|||
|
|
@ -22,7 +22,7 @@ compute 1 all centro/atom :pre
|
|||
[Description:]
|
||||
|
||||
Define a computation that calculates the centro-symmetry parameter for
|
||||
each atom in a group. In solid-state systems the centro-symmetry
|
||||
each atom in the group. In solid-state systems the centro-symmetry
|
||||
parameter is a useful measure of the local lattice disorder around an
|
||||
atom and can be used to characterize whether the atom is part of a
|
||||
perfect lattice, a local defect (e.g. a dislocation or stacking
|
||||
|
|
@ -42,9 +42,9 @@ nearest neighbors. Atoms not in the group are included in the 12
|
|||
neighbors used in this calculation.
|
||||
|
||||
The neighbor list needed to compute this quantity is constructed each
|
||||
time the calculation is performed (i.e. each time a snapshot of atoms
|
||||
time the calculation is performed (e.g. each time a snapshot of atoms
|
||||
is dumped). Thus it can be inefficient to compute/dump this quantity
|
||||
too frequently or to have multiple compute/dump commands, each of a
|
||||
too frequently or to have multiple compute/dump commands, each with a
|
||||
{centro/atom} style.
|
||||
|
||||
[Output info:]
|
||||
|
|
@ -56,7 +56,9 @@ output options.
|
|||
|
||||
[Restrictions:] none
|
||||
|
||||
[Related commands:] none
|
||||
[Related commands:]
|
||||
|
||||
"compute cna/atom"_compute_cna_atom.html
|
||||
|
||||
[Default:] none
|
||||
|
||||
|
|
|
|||
|
|
@ -0,0 +1,101 @@
|
|||
<HTML>
|
||||
<CENTER><A HREF = "http://lammps.sandia.gov">LAMMPS WWW Site</A> - <A HREF = "Manual.html">LAMMPS Documentation</A> - <A HREF = "Section_commands.html#comm">LAMMPS Commands</A>
|
||||
</CENTER>
|
||||
|
||||
|
||||
|
||||
|
||||
|
||||
|
||||
<HR>
|
||||
|
||||
<H3>compute cna/atom command
|
||||
</H3>
|
||||
<P><B>Syntax:</B>
|
||||
</P>
|
||||
<PRE>compute ID group-ID cna/atom cutoff
|
||||
</PRE>
|
||||
<UL><LI>ID, group-ID are documented in <A HREF = "compute.html">compute</A> command
|
||||
<LI>cna/atom = style name of this compute command
|
||||
<LI>cutoff = cutoff distance for nearest neighbors (distance units)
|
||||
</UL>
|
||||
<P><B>Examples:</B>
|
||||
</P>
|
||||
<PRE>compute 1 all cna/atom 3.08
|
||||
</PRE>
|
||||
<P><B>Description:</B>
|
||||
</P>
|
||||
<P>Define a computation that calculates the CNA (Common Neighbor
|
||||
Analysis) pattern for each atom in the group. In solid-state systems
|
||||
the CNA pattern is a useful measure of the local crystal structure
|
||||
around an atom. The CNA methodology is described in <A HREF = "#Faken">(Faken)</A>
|
||||
and <A HREF = "#Tsuzuki">(Tsuzuki)</A>.
|
||||
</P>
|
||||
<P>Currently, there are five kinds of CNA patterns LAMMPS recognizes:
|
||||
</P>
|
||||
<UL><LI>fcc = 1
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||||
<LI>hcp = 2
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||||
<LI>bcc = 3
|
||||
<LI>icosohedral = 4
|
||||
<LI>unknown = 5
|
||||
</UL>
|
||||
<P>The value of the CNA pattern will be 0 for atoms not in the specified
|
||||
compute group. Note that normally a CNA calculation should only be be
|
||||
performed on mono-component systems.
|
||||
</P>
|
||||
<P>The CNA calculation can be sensitive to the specified cutoff value.
|
||||
You should insure the appropriate nearest neighbors of an atom are
|
||||
found within the cutoff distance for the presumed crystal strucure.
|
||||
E.g. 12 nearest neighbor for perfect FCC and HCP crystals, 14 nearest
|
||||
neighbors for perfect BCC crystals. These formulas can be used to
|
||||
obtain a good cutoff distance:
|
||||
</P>
|
||||
<CENTER><IMG SRC = "Eqs/cna_cutoff1.jpg">
|
||||
</CENTER>
|
||||
<P>where a is the lattice constant for the crystal structure concerned
|
||||
and in the HCP case, x = (c/a) / 1.633, where 1.633 is the ideal c/a
|
||||
for HCP crystals.
|
||||
</P>
|
||||
<P>Also note that since the CNA calculation in LAMMPS uses the neighbors
|
||||
of an owned atom to find the nearest neighbors of a ghost atom, the
|
||||
following relation should also be satisfied:
|
||||
</P>
|
||||
<CENTER><IMG SRC = "Eqs/cna_cutoff2.jpg">
|
||||
</CENTER>
|
||||
<P>where Rc is the cutoff distance of the potential, Rs is the skin
|
||||
distance as specified by the <A HREF = "neighbor.html">neighbor</A> command, and
|
||||
cutoff is the argument used with the compute cna/atom command. LAMMPS
|
||||
will issue a warning if this is not the case.
|
||||
</P>
|
||||
<P>The neighbor list needed to compute this quantity is constructed each
|
||||
time the calculation is performed (e.g. each time a snapshot of atoms
|
||||
is dumped). Thus it can be inefficient to compute/dump this quantity
|
||||
too frequently or to have multiple compute/dump commands, each with a
|
||||
<I>cna/atom</I> style.
|
||||
</P>
|
||||
<P><B>Output info:</B>
|
||||
</P>
|
||||
<P>This compute calculates a scalar quantity for each atom, which can be
|
||||
accessed by any command that uses per-atom computes as input. See
|
||||
<A HREF = "Section_howto.html#4_15">this section</A> for an overview of LAMMPS
|
||||
output options.
|
||||
</P>
|
||||
<P><B>Restrictions:</B> none
|
||||
</P>
|
||||
<P><B>Related commands:</B>
|
||||
</P>
|
||||
<P><A HREF = "compute_centro_atom.html">compute centro/atom</A>
|
||||
</P>
|
||||
<P><B>Default:</B> none
|
||||
</P>
|
||||
<HR>
|
||||
|
||||
<A NAME = "Faken"></A>
|
||||
|
||||
<P><B>(Faken)</B> Faken, Jonsson, Comput Mater Sci, 2, 279 (1994).
|
||||
</P>
|
||||
<A NAME = "Tsuzuki"></A>
|
||||
|
||||
<P><B>(Tsuzuki)</B> Tsuzuki, Branicio, Rino, Comput Phys Comm, 177, 518 (2007).
|
||||
</P>
|
||||
</HTML>
|
||||
|
|
@ -0,0 +1,94 @@
|
|||
"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
|
||||
|
||||
compute cna/atom command :h3
|
||||
|
||||
[Syntax:]
|
||||
|
||||
compute ID group-ID cna/atom cutoff :pre
|
||||
|
||||
ID, group-ID are documented in "compute"_compute.html command
|
||||
cna/atom = style name of this compute command
|
||||
cutoff = cutoff distance for nearest neighbors (distance units) :ul
|
||||
|
||||
[Examples:]
|
||||
|
||||
compute 1 all cna/atom 3.08 :pre
|
||||
|
||||
[Description:]
|
||||
|
||||
Define a computation that calculates the CNA (Common Neighbor
|
||||
Analysis) pattern for each atom in the group. In solid-state systems
|
||||
the CNA pattern is a useful measure of the local crystal structure
|
||||
around an atom. The CNA methodology is described in "(Faken)"_#Faken
|
||||
and "(Tsuzuki)"_#Tsuzuki.
|
||||
|
||||
Currently, there are five kinds of CNA patterns LAMMPS recognizes:
|
||||
|
||||
fcc = 1
|
||||
hcp = 2
|
||||
bcc = 3
|
||||
icosohedral = 4
|
||||
unknown = 5 :ul
|
||||
|
||||
The value of the CNA pattern will be 0 for atoms not in the specified
|
||||
compute group. Note that normally a CNA calculation should only be be
|
||||
performed on mono-component systems.
|
||||
|
||||
The CNA calculation can be sensitive to the specified cutoff value.
|
||||
You should insure the appropriate nearest neighbors of an atom are
|
||||
found within the cutoff distance for the presumed crystal strucure.
|
||||
E.g. 12 nearest neighbor for perfect FCC and HCP crystals, 14 nearest
|
||||
neighbors for perfect BCC crystals. These formulas can be used to
|
||||
obtain a good cutoff distance:
|
||||
|
||||
:c,image(Eqs/cna_cutoff1.jpg)
|
||||
|
||||
where a is the lattice constant for the crystal structure concerned
|
||||
and in the HCP case, x = (c/a) / 1.633, where 1.633 is the ideal c/a
|
||||
for HCP crystals.
|
||||
|
||||
Also note that since the CNA calculation in LAMMPS uses the neighbors
|
||||
of an owned atom to find the nearest neighbors of a ghost atom, the
|
||||
following relation should also be satisfied:
|
||||
|
||||
:c,image(Eqs/cna_cutoff2.jpg)
|
||||
|
||||
where Rc is the cutoff distance of the potential, Rs is the skin
|
||||
distance as specified by the "neighbor"_neighbor.html command, and
|
||||
cutoff is the argument used with the compute cna/atom command. LAMMPS
|
||||
will issue a warning if this is not the case.
|
||||
|
||||
The neighbor list needed to compute this quantity is constructed each
|
||||
time the calculation is performed (e.g. each time a snapshot of atoms
|
||||
is dumped). Thus it can be inefficient to compute/dump this quantity
|
||||
too frequently or to have multiple compute/dump commands, each with a
|
||||
{cna/atom} style.
|
||||
|
||||
[Output info:]
|
||||
|
||||
This compute calculates a scalar quantity for each atom, which can be
|
||||
accessed by any command that uses per-atom computes as input. See
|
||||
"this section"_Section_howto.html#4_15 for an overview of LAMMPS
|
||||
output options.
|
||||
|
||||
[Restrictions:] none
|
||||
|
||||
[Related commands:]
|
||||
|
||||
"compute centro/atom"_compute_centro_atom.html
|
||||
|
||||
[Default:] none
|
||||
|
||||
:line
|
||||
|
||||
:link(Faken)
|
||||
[(Faken)] Faken, Jonsson, Comput Mater Sci, 2, 279 (1994).
|
||||
|
||||
:link(Tsuzuki)
|
||||
[(Tsuzuki)] Tsuzuki, Branicio, Rino, Comput Phys Comm, 177, 518 (2007).
|
||||
|
|
@ -106,11 +106,6 @@ atoms do not overlap existing atoms inappropriately. The
|
|||
<A HREF = "delete_atoms.html">delete_atoms</A> command can be used to handle
|
||||
overlaps.
|
||||
</P>
|
||||
<P>Aside from their position and atom type, other properties of created
|
||||
atoms are set to 0.0, e.g velocity, charge, etc. These properties can
|
||||
be changed via the <A HREF = "velocity.html">velocity</A> or <A HREF = "set.html">set</A>
|
||||
commands.
|
||||
</P>
|
||||
<P>Atom IDs are assigned to created atoms in the following way. The
|
||||
collection of created atoms are assigned consecutive IDs that start
|
||||
immediately following the largest atom ID existing before the
|
||||
|
|
@ -118,6 +113,29 @@ create_atoms command was invoked. When a simulation is performed on
|
|||
different numbers of processors, there is no guarantee a particular
|
||||
created atom will be assigned the same ID.
|
||||
</P>
|
||||
<P>Aside from their ID, atom type, and xyz position, other properties of
|
||||
created atoms are set to default values, depending on which quantities
|
||||
are defined by the chosen <A HREF = "atom_style.html">atom style</A>. See the <A HREF = "atom_style.html">atom
|
||||
style</A> command for more details. See the
|
||||
<A HREF = "set.html">set</A> and <A HREF = "velocity.html">velocity</A> commands for info on how
|
||||
to change these values.
|
||||
</P>
|
||||
<UL><LI>charge = 0.0
|
||||
<LI>dipole moment = 0.0
|
||||
<LI>diameter = 1.0
|
||||
<LI>volume = 1.0
|
||||
<LI>density = 1.0
|
||||
<LI>velocity = 0.0
|
||||
<LI>angular velocity = 0.0
|
||||
<LI>angular momentum = 0.0
|
||||
<LI>quaternion = (1,0,0,0)
|
||||
<LI>bonds, angles, dihedrals, impropers = none
|
||||
</UL>
|
||||
<P>The <I>granular</I> style sets the diameter and density to 1.0 and
|
||||
calculates a mass for the particle, which is PI/6 * diameter^3 =
|
||||
0.5236. The <I>peri</I> style sets the volume and density to 1.0 and
|
||||
calculates a mass for the particle, which is also 1.0.
|
||||
</P>
|
||||
<P><B>Restrictions:</B>
|
||||
</P>
|
||||
<P>An <A HREF = "atom_style.html">atom_style</A> must be previously defined to use this
|
||||
|
|
|
|||
|
|
@ -97,11 +97,6 @@ atoms do not overlap existing atoms inappropriately. The
|
|||
"delete_atoms"_delete_atoms.html command can be used to handle
|
||||
overlaps.
|
||||
|
||||
Aside from their position and atom type, other properties of created
|
||||
atoms are set to 0.0, e.g velocity, charge, etc. These properties can
|
||||
be changed via the "velocity"_velocity.html or "set"_set.html
|
||||
commands.
|
||||
|
||||
Atom IDs are assigned to created atoms in the following way. The
|
||||
collection of created atoms are assigned consecutive IDs that start
|
||||
immediately following the largest atom ID existing before the
|
||||
|
|
@ -109,6 +104,29 @@ create_atoms command was invoked. When a simulation is performed on
|
|||
different numbers of processors, there is no guarantee a particular
|
||||
created atom will be assigned the same ID.
|
||||
|
||||
Aside from their ID, atom type, and xyz position, other properties of
|
||||
created atoms are set to default values, depending on which quantities
|
||||
are defined by the chosen "atom style"_atom_style.html. See the "atom
|
||||
style"_atom_style.html command for more details. See the
|
||||
"set"_set.html and "velocity"_velocity.html commands for info on how
|
||||
to change these values.
|
||||
|
||||
charge = 0.0
|
||||
dipole moment = 0.0
|
||||
diameter = 1.0
|
||||
volume = 1.0
|
||||
density = 1.0
|
||||
velocity = 0.0
|
||||
angular velocity = 0.0
|
||||
angular momentum = 0.0
|
||||
quaternion = (1,0,0,0)
|
||||
bonds, angles, dihedrals, impropers = none :ul
|
||||
|
||||
The {granular} style sets the diameter and density to 1.0 and
|
||||
calculates a mass for the particle, which is PI/6 * diameter^3 =
|
||||
0.5236. The {peri} style sets the volume and density to 1.0 and
|
||||
calculates a mass for the particle, which is also 1.0.
|
||||
|
||||
[Restrictions:]
|
||||
|
||||
An "atom_style"_atom_style.html must be previously defined to use this
|
||||
|
|
|
|||
|
|
@ -27,46 +27,58 @@ mass 2* 62.5
|
|||
<P><B>Description:</B>
|
||||
</P>
|
||||
<P>Set the mass for all atoms of one or more atom types. Mass values can
|
||||
also be set in the <A HREF = "read_data.html">read_data</A> data file. See the
|
||||
<A HREF = "units.html">units</A> command for what mass units to use.
|
||||
also be set in the <A HREF = "read_data.html">read_data</A> data file using the
|
||||
"Masses" keyword. See the <A HREF = "units.html">units</A> command for what mass
|
||||
units to use.
|
||||
</P>
|
||||
<P>Most atom styles require per-type masses to be specified. One
|
||||
exception is <A HREF = "atom_style.html">atom_style granular</A> or <A HREF = "atom_style.html">atom_style
|
||||
peri</A>, where masses are defined for individual atoms,
|
||||
not types. These are defined in the file read by the
|
||||
<A HREF = "read_data.html">read_data</A> command, or set to default values by the
|
||||
<A HREF = "create_atoms.html">create_atoms</A> command, or set to new values by the
|
||||
<A HREF = "set.html">set density</A> command. Also note that <A HREF = "pair_eam.html">pair_style
|
||||
eam</A> defines the masses of atom types in the EAM
|
||||
potential file.
|
||||
<P>The I index can be specified in one of two ways. An explicit numeric
|
||||
value can be used, as in the 1st example above. Or a wild-card
|
||||
asterisk can be used to set the mass for multiple atom types. This
|
||||
takes the form "*" or "*n" or "n*" or "m*n". If N = the number of
|
||||
atom types, then an asterisk with no numeric values means all types
|
||||
from 1 to N. A leading asterisk means all types from 1 to n
|
||||
(inclusive). A trailing asterisk means all types from n to N
|
||||
(inclusive). A middle asterisk means all types from m to n
|
||||
(inclusive).
|
||||
</P>
|
||||
<P>I can be specified in one of two ways. An explicit numeric value can
|
||||
be used, as in the 1st example above. Or a wild-card asterisk can be
|
||||
used to set the mass for multiple atom types. This takes the form "*"
|
||||
or "*n" or "n*" or "m*n". If N = the number of atom types, then an
|
||||
asterisk with no numeric values means all types from 1 to N. A leading
|
||||
asterisk means all types from 1 to n (inclusive). A trailing asterisk
|
||||
means all types from n to N (inclusive). A middle asterisk means all
|
||||
types from m to n (inclusive).
|
||||
</P>
|
||||
<P>A line in a data file that specifies mass uses the same format as the
|
||||
arguments of the mass command in an input script, except that no
|
||||
wild-card asterisk can be used. For example, under the "Masses"
|
||||
section of a data file, the line that corresponds to the 1st example
|
||||
above would be listed as
|
||||
<P>A line in a <A HREF = "read_data.html">data file</A> that follows the "Masses"
|
||||
keyword specifies mass using the same format as the arguments of the
|
||||
mass command in an input script, except that no wild-card asterisk can
|
||||
be used. For example, under the "Masses" section of a data file, the
|
||||
line that corresponds to the 1st example above would be listed as
|
||||
</P>
|
||||
<PRE>1 1.0
|
||||
</PRE>
|
||||
<P>Note that the mass command can only be used if the <A HREF = "atom_style.html">atom
|
||||
style</A> requires per-type atom mass to be set, which
|
||||
most do. Exceptions are <A HREF = "atom_style.html">atom_style granular</A> or
|
||||
<A HREF = "atom_style.html">atom_style peri</A>, which require mass to be set for
|
||||
individual particles, not types. Per-atom masses are defined in the
|
||||
data file read by the <A HREF = "read_data.html">read_data</A> command, or set to
|
||||
default values by the <A HREF = "create_atoms.html">create_atoms</A> command, or set
|
||||
to new values by the <A HREF = "set.html">set density</A> command.
|
||||
</P>
|
||||
<P>Also note that <A HREF = "pair_eam.html">pair_style eam</A> defines the masses of
|
||||
atom types in the EAM potential file, in which case the mass command
|
||||
is normally not used.
|
||||
</P>
|
||||
<P>If you define a <A HREF = "atom_style.html">hybrid atom style</A> which includes one
|
||||
(or more) sub-styles which require per-type mass and one (or more)
|
||||
sub-styles which require per-atom mass, then you must define both.
|
||||
However, the per-type mass is ignored in this case; only the per-atom
|
||||
mass is used.
|
||||
</P>
|
||||
<P><B>Restrictions:</B>
|
||||
</P>
|
||||
<P>This command must come after the simulation box is defined by a
|
||||
<A HREF = "read_data.html">read_data</A>, <A HREF = "read_restart.html">read_restart</A>, or
|
||||
<A HREF = "create_box.html">create_box</A> command.
|
||||
</P>
|
||||
<P>All masses must be defined before a simulation is run (if the atom
|
||||
style requires masses be set). They must also all be defined before a
|
||||
<A HREF = "velocity.html">velocity</A> or <A HREF = "fix_shake.html">fix shake</A> command is
|
||||
used.
|
||||
<P>All masses must be defined before a simulation is run. They must also
|
||||
all be defined before a <A HREF = "velocity.html">velocity</A> or <A HREF = "fix_shake.html">fix
|
||||
shake</A> command is used.
|
||||
</P>
|
||||
<P>The mass assigned to any type or atom must be > 0.0.
|
||||
</P>
|
||||
<P><B>Related commands:</B> none
|
||||
</P>
|
||||
|
|
|
|||
70
doc/mass.txt
70
doc/mass.txt
|
|
@ -24,46 +24,58 @@ mass 2* 62.5 :pre
|
|||
[Description:]
|
||||
|
||||
Set the mass for all atoms of one or more atom types. Mass values can
|
||||
also be set in the "read_data"_read_data.html data file. See the
|
||||
"units"_units.html command for what mass units to use.
|
||||
also be set in the "read_data"_read_data.html data file using the
|
||||
"Masses" keyword. See the "units"_units.html command for what mass
|
||||
units to use.
|
||||
|
||||
Most atom styles require per-type masses to be specified. One
|
||||
exception is "atom_style granular"_atom_style.html or "atom_style
|
||||
peri"_atom_style.html, where masses are defined for individual atoms,
|
||||
not types. These are defined in the file read by the
|
||||
"read_data"_read_data.html command, or set to default values by the
|
||||
"create_atoms"_create_atoms.html command, or set to new values by the
|
||||
"set density"_set.html command. Also note that "pair_style
|
||||
eam"_pair_eam.html defines the masses of atom types in the EAM
|
||||
potential file.
|
||||
The I index can be specified in one of two ways. An explicit numeric
|
||||
value can be used, as in the 1st example above. Or a wild-card
|
||||
asterisk can be used to set the mass for multiple atom types. This
|
||||
takes the form "*" or "*n" or "n*" or "m*n". If N = the number of
|
||||
atom types, then an asterisk with no numeric values means all types
|
||||
from 1 to N. A leading asterisk means all types from 1 to n
|
||||
(inclusive). A trailing asterisk means all types from n to N
|
||||
(inclusive). A middle asterisk means all types from m to n
|
||||
(inclusive).
|
||||
|
||||
I can be specified in one of two ways. An explicit numeric value can
|
||||
be used, as in the 1st example above. Or a wild-card asterisk can be
|
||||
used to set the mass for multiple atom types. This takes the form "*"
|
||||
or "*n" or "n*" or "m*n". If N = the number of atom types, then an
|
||||
asterisk with no numeric values means all types from 1 to N. A leading
|
||||
asterisk means all types from 1 to n (inclusive). A trailing asterisk
|
||||
means all types from n to N (inclusive). A middle asterisk means all
|
||||
types from m to n (inclusive).
|
||||
|
||||
A line in a data file that specifies mass uses the same format as the
|
||||
arguments of the mass command in an input script, except that no
|
||||
wild-card asterisk can be used. For example, under the "Masses"
|
||||
section of a data file, the line that corresponds to the 1st example
|
||||
above would be listed as
|
||||
A line in a "data file"_read_data.html that follows the "Masses"
|
||||
keyword specifies mass using the same format as the arguments of the
|
||||
mass command in an input script, except that no wild-card asterisk can
|
||||
be used. For example, under the "Masses" section of a data file, the
|
||||
line that corresponds to the 1st example above would be listed as
|
||||
|
||||
1 1.0 :pre
|
||||
|
||||
Note that the mass command can only be used if the "atom
|
||||
style"_atom_style.html requires per-type atom mass to be set, which
|
||||
most do. Exceptions are "atom_style granular"_atom_style.html or
|
||||
"atom_style peri"_atom_style.html, which require mass to be set for
|
||||
individual particles, not types. Per-atom masses are defined in the
|
||||
data file read by the "read_data"_read_data.html command, or set to
|
||||
default values by the "create_atoms"_create_atoms.html command, or set
|
||||
to new values by the "set density"_set.html command.
|
||||
|
||||
Also note that "pair_style eam"_pair_eam.html defines the masses of
|
||||
atom types in the EAM potential file, in which case the mass command
|
||||
is normally not used.
|
||||
|
||||
If you define a "hybrid atom style"_atom_style.html which includes one
|
||||
(or more) sub-styles which require per-type mass and one (or more)
|
||||
sub-styles which require per-atom mass, then you must define both.
|
||||
However, the per-type mass is ignored in this case; only the per-atom
|
||||
mass is used.
|
||||
|
||||
[Restrictions:]
|
||||
|
||||
This command must come after the simulation box is defined by a
|
||||
"read_data"_read_data.html, "read_restart"_read_restart.html, or
|
||||
"create_box"_create_box.html command.
|
||||
|
||||
All masses must be defined before a simulation is run (if the atom
|
||||
style requires masses be set). They must also all be defined before a
|
||||
"velocity"_velocity.html or "fix shake"_fix_shake.html command is
|
||||
used.
|
||||
All masses must be defined before a simulation is run. They must also
|
||||
all be defined before a "velocity"_velocity.html or "fix
|
||||
shake"_fix_shake.html command is used.
|
||||
|
||||
The mass assigned to any type or atom must be > 0.0.
|
||||
|
||||
[Related commands:] none
|
||||
|
||||
|
|
|
|||
|
|
@ -16,9 +16,9 @@
|
|||
<PRE>shape I x y z
|
||||
</PRE>
|
||||
<UL><LI>I = atom type (see asterisk form below)
|
||||
<LI>x = x diameter
|
||||
<LI>y = y diameter
|
||||
<LI>z = z diameter
|
||||
<LI>x = x diameter (distance units)
|
||||
<LI>y = y diameter (distance units)
|
||||
<LI>z = z diameter (distance units)
|
||||
</UL>
|
||||
<P><B>Examples:</B>
|
||||
</P>
|
||||
|
|
@ -28,25 +28,11 @@ shape 2* 3.0 1.0 1.0
|
|||
</PRE>
|
||||
<P><B>Description:</B>
|
||||
</P>
|
||||
<P>Set the shape for all atoms of one or more atom types. Shape values
|
||||
can also be set in the <A HREF = "read_data.html">read_data</A> data file. See the
|
||||
<A HREF = "units.html">units</A> command for what distance units to use.
|
||||
</P>
|
||||
<P>Currently, only <A HREF = "atom_style.html">atom_style dipole</A> and <A HREF = "atom_style.html">atom_style
|
||||
ellipsoid</A> require that shapes be set.
|
||||
</P>
|
||||
<P>Dipoles use the atom shape to compute a moment of inertia for
|
||||
rotational energy. Only the 1st component of the shape is used since
|
||||
the particles are assumed to be spherical. The value of the first
|
||||
component should be the same as the Lennard-Jones sigma value defined
|
||||
in the dipole pair potential, i.e. in <A HREF = "pair_dipole.html">pair_style
|
||||
dipole</A>.
|
||||
</P>
|
||||
<P>Ellipsoids use the atom shape to compute a generalized inertia tensor.
|
||||
For example, a shape setting of 3.0 1.0 1.0 defines a particle 3x
|
||||
longer in x than in y or z and with a circular cross-section in yz.
|
||||
Ellipsoids that are spherical can be defined by setting all 3 shape
|
||||
components the same.
|
||||
<P>Set the shape for all atoms of one or more atom types. In LAMMPS,
|
||||
particles that have a finite size are said to have a "shape", as
|
||||
opposed to being a point mass. Shape values can also be set in the
|
||||
<A HREF = "read_data.html">read_data</A> data file using the "Shapes" keyword. See
|
||||
the <A HREF = "units.html">units</A> command for what distance units to use.
|
||||
</P>
|
||||
<P>The I index can be specified in one of two ways. An explicit numeric
|
||||
value can be used, as in the 1st example above. Or a wild-card
|
||||
|
|
@ -58,14 +44,48 @@ from 1 to N. A leading asterisk means all types from 1 to n
|
|||
(inclusive). A middle asterisk means all types from m to n
|
||||
(inclusive).
|
||||
</P>
|
||||
<P>A line in a data file that specifies shape uses the same format as the
|
||||
arguments of the shape command in an input script, except that no
|
||||
wild-card asterisk can be used. For example, under the "Shapes"
|
||||
section of a data file, the line that corresponds to the 1st example
|
||||
above would be listed as
|
||||
<P>A line in a <A HREF = "read_data.html">data file</A> that follows the "Shapes"
|
||||
keyword specifies shape using the same format as the arguments of the
|
||||
shape command in an input script, except that no wild-card asterisk
|
||||
can be used. For example, under the "Shapes" section of a data file,
|
||||
the line that corresponds to the 1st example above would be listed as
|
||||
</P>
|
||||
<PRE>1 1.0 1.0 1.0
|
||||
</PRE>
|
||||
<P>The shape values can be set to 0.0, which means that atoms of that
|
||||
type are point masses and not finite-size particles. Pair styles and
|
||||
fixes that rely on particles having a finite size should not be used
|
||||
for such particles.
|
||||
</P>
|
||||
<P>Note that the shape command can only be used if the <A HREF = "atom_style.html">atom
|
||||
style</A> requires per-type atom shape to be set.
|
||||
Currently, only the <I>dipole</I> and <I>ellipsoid</I> styles do. The
|
||||
<I>granular</I> and <I>peri</I> styles require the shape to be set for indivual
|
||||
particles, not types. For these styles, the only option currently
|
||||
allowed is for spherical particles, so a single diameter value
|
||||
suffices to determine the shape. Per-atom diameters are defined in
|
||||
the data file read by the <A HREF = "read_data.html">read_data</A> command, or set
|
||||
to default values by the <A HREF = "create_atoms.html">create_atoms</A> command, or
|
||||
set to new values by the <A HREF = "set.html">set diamter</A> command.
|
||||
</P>
|
||||
<P>Dipoles use the atom shape to compute a moment of inertia for
|
||||
rotational energy. See the <A HREF = "pair_dipole.html">pair_style dipole</A>
|
||||
command. Only the 1st component of the shape is used since the
|
||||
particles are assumed to be spherical.
|
||||
</P>
|
||||
<P>Ellipsoids use the atom shape to compute a generalized inertia tensor.
|
||||
For example, a shape setting of 3.0 1.0 1.0 defines a particle 3x
|
||||
longer in x than in y or z and with a circular cross-section in yz.
|
||||
Degenerate ellipsoids which are spherical can be defined by setting
|
||||
all 3 shape components the same.
|
||||
</P>
|
||||
<P>If you define a <A HREF = "atom_style.html">hybrid atom style</A> which includes one
|
||||
(or more) sub-styles which require per-type shape and one (or more)
|
||||
sub-styles which require per-atom shape, then you must define both.
|
||||
If the per-atom diameter is set to 0.0, the per-type shape is used.
|
||||
If the per-atom diameter is non-zero, then the per-type shape is
|
||||
ignored.
|
||||
</P>
|
||||
<P><B>Restrictions:</B>
|
||||
</P>
|
||||
<P>This command must come after the simulation box is defined by a
|
||||
|
|
|
|||
|
|
@ -13,9 +13,9 @@ shape command :h3
|
|||
shape I x y z :pre
|
||||
|
||||
I = atom type (see asterisk form below)
|
||||
x = x diameter
|
||||
y = y diameter
|
||||
z = z diameter :ul
|
||||
x = x diameter (distance units)
|
||||
y = y diameter (distance units)
|
||||
z = z diameter (distance units) :ul
|
||||
|
||||
[Examples:]
|
||||
|
||||
|
|
@ -25,25 +25,11 @@ shape 2* 3.0 1.0 1.0 :pre
|
|||
|
||||
[Description:]
|
||||
|
||||
Set the shape for all atoms of one or more atom types. Shape values
|
||||
can also be set in the "read_data"_read_data.html data file. See the
|
||||
"units"_units.html command for what distance units to use.
|
||||
|
||||
Currently, only "atom_style dipole"_atom_style.html and "atom_style
|
||||
ellipsoid"_atom_style.html require that shapes be set.
|
||||
|
||||
Dipoles use the atom shape to compute a moment of inertia for
|
||||
rotational energy. Only the 1st component of the shape is used since
|
||||
the particles are assumed to be spherical. The value of the first
|
||||
component should be the same as the Lennard-Jones sigma value defined
|
||||
in the dipole pair potential, i.e. in "pair_style
|
||||
dipole"_pair_dipole.html.
|
||||
|
||||
Ellipsoids use the atom shape to compute a generalized inertia tensor.
|
||||
For example, a shape setting of 3.0 1.0 1.0 defines a particle 3x
|
||||
longer in x than in y or z and with a circular cross-section in yz.
|
||||
Ellipsoids that are spherical can be defined by setting all 3 shape
|
||||
components the same.
|
||||
Set the shape for all atoms of one or more atom types. In LAMMPS,
|
||||
particles that have a finite size are said to have a "shape", as
|
||||
opposed to being a point mass. Shape values can also be set in the
|
||||
"read_data"_read_data.html data file using the "Shapes" keyword. See
|
||||
the "units"_units.html command for what distance units to use.
|
||||
|
||||
The I index can be specified in one of two ways. An explicit numeric
|
||||
value can be used, as in the 1st example above. Or a wild-card
|
||||
|
|
@ -55,14 +41,48 @@ from 1 to N. A leading asterisk means all types from 1 to n
|
|||
(inclusive). A middle asterisk means all types from m to n
|
||||
(inclusive).
|
||||
|
||||
A line in a data file that specifies shape uses the same format as the
|
||||
arguments of the shape command in an input script, except that no
|
||||
wild-card asterisk can be used. For example, under the "Shapes"
|
||||
section of a data file, the line that corresponds to the 1st example
|
||||
above would be listed as
|
||||
A line in a "data file"_read_data.html that follows the "Shapes"
|
||||
keyword specifies shape using the same format as the arguments of the
|
||||
shape command in an input script, except that no wild-card asterisk
|
||||
can be used. For example, under the "Shapes" section of a data file,
|
||||
the line that corresponds to the 1st example above would be listed as
|
||||
|
||||
1 1.0 1.0 1.0 :pre
|
||||
|
||||
The shape values can be set to 0.0, which means that atoms of that
|
||||
type are point masses and not finite-size particles. Pair styles and
|
||||
fixes that rely on particles having a finite size should not be used
|
||||
for such particles.
|
||||
|
||||
Note that the shape command can only be used if the "atom
|
||||
style"_atom_style.html requires per-type atom shape to be set.
|
||||
Currently, only the {dipole} and {ellipsoid} styles do. The
|
||||
{granular} and {peri} styles require the shape to be set for indivual
|
||||
particles, not types. For these styles, the only option currently
|
||||
allowed is for spherical particles, so a single diameter value
|
||||
suffices to determine the shape. Per-atom diameters are defined in
|
||||
the data file read by the "read_data"_read_data.html command, or set
|
||||
to default values by the "create_atoms"_create_atoms.html command, or
|
||||
set to new values by the "set diamter"_set.html command.
|
||||
|
||||
Dipoles use the atom shape to compute a moment of inertia for
|
||||
rotational energy. See the "pair_style dipole"_pair_dipole.html
|
||||
command. Only the 1st component of the shape is used since the
|
||||
particles are assumed to be spherical.
|
||||
|
||||
Ellipsoids use the atom shape to compute a generalized inertia tensor.
|
||||
For example, a shape setting of 3.0 1.0 1.0 defines a particle 3x
|
||||
longer in x than in y or z and with a circular cross-section in yz.
|
||||
Degenerate ellipsoids which are spherical can be defined by setting
|
||||
all 3 shape components the same.
|
||||
|
||||
If you define a "hybrid atom style"_atom_style.html which includes one
|
||||
(or more) sub-styles which require per-type shape and one (or more)
|
||||
sub-styles which require per-atom shape, then you must define both.
|
||||
If the per-atom diameter is set to 0.0, the per-type shape is used.
|
||||
If the per-atom diameter is non-zero, then the per-type shape is
|
||||
ignored.
|
||||
|
||||
[Restrictions:]
|
||||
|
||||
This command must come after the simulation box is defined by a
|
||||
|
|
|
|||
Loading…
Reference in New Issue