forked from lijiext/lammps
git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@1246 f3b2605a-c512-4ea7-a41b-209d697bcdaa
This commit is contained in:
parent
d33f6f99a3
commit
c30a5382d8
|
@ -248,7 +248,11 @@ integers (1, not 1.0).
|
|||
</UL>
|
||||
<P>An <I>Atoms</I> section must appear in the data file if natoms > 0 in the
|
||||
header section. The atoms can be listed in any order. These are the
|
||||
line formats for each <A HREF = "atom_style.html">atom style</A> in LAMMPS:
|
||||
line formats for each <A HREF = "atom_style.html">atom style</A> in LAMMPS. As
|
||||
discussed below, each line can optionally have 3 flags (nx,ny,nz)
|
||||
appended to it, which indicate which image of a periodic simulation
|
||||
box the atom is in. These may be important to include for some kinds
|
||||
of analysis.
|
||||
</P>
|
||||
<DIV ALIGN=center><TABLE BORDER=1 >
|
||||
<TR><TD >angle</TD><TD > atom-ID molecule-ID atom-type x y z</TD></TR>
|
||||
|
@ -264,7 +268,7 @@ line formats for each <A HREF = "atom_style.html">atom style</A> in LAMMPS:
|
|||
<TR><TD >hybrid</TD><TD > atom-ID atom-type x y z sub-style1 sub-style2 ...
|
||||
</TD></TR></TABLE></DIV>
|
||||
|
||||
<P>where the keywords have these meanings:
|
||||
<P>The keywords have these meanings:
|
||||
</P>
|
||||
<UL><LI>atom-ID = integer ID of atom
|
||||
<LI>molecule-ID = integer ID of molecule the atom belongs to
|
||||
|
@ -327,20 +331,29 @@ listed in the same order they appear as listed above.
|
|||
</P>
|
||||
<PRE>atom-ID atom-type x y z q diameter density
|
||||
</PRE>
|
||||
<P>Atom lines (all lines or none of them) can optionally list 3 final
|
||||
<P>Atom lines (all lines or none of them) can optionally list 3 trailing
|
||||
integer values: nx,ny,nz. For periodic dimensions, they specify which
|
||||
image of the box the atom is considered to be in. An image of 0 means
|
||||
the box as defined. A value of 2 means add 2 box lengths to get the
|
||||
true value. A value of -1 means subtract 1 box length to get the true
|
||||
value. LAMMPS updates these flags as atoms cross periodic boundaries
|
||||
during the simulation. The flags can be output with atom snapshots
|
||||
via the <A HREF = "dump.html">dump</A> command. If nx,ny,nz values are not set in
|
||||
the data file, LAMMPS initializes them to 0.
|
||||
it is inside the box as defined. A value of 2 means add 2 box lengths
|
||||
to get the true value. A value of -1 means subtract 1 box length to
|
||||
get the true value. LAMMPS updates these flags as atoms cross
|
||||
periodic boundaries during the simulation. The flags can be output
|
||||
with atom snapshots via the <A HREF = "dump.html">dump</A> command.
|
||||
</P>
|
||||
<P>If nx,ny,nz values are not set in the data file, LAMMPS initializes
|
||||
them to 0. If image information is needed for later analysis and they
|
||||
are not all initially 0, it's important to set them correctly in the
|
||||
data file. Also, if you plan to use the <A HREF = "replicate.html">replicate</A>
|
||||
command to generate a larger system, these flags must be listed
|
||||
correctly for bonded atoms when the bond crosses a periodic boundary.
|
||||
I.e. the values of the image flags should be different by 1 (in the
|
||||
appropriate dimension) for the two atoms in such a bond.
|
||||
</P>
|
||||
<P>Atom velocities and other atom quantities not defined above are set to
|
||||
0.0 when the <I>Atoms</I> section is read. They may later be set by a
|
||||
<I>Velocities</I> section in the data file or by a <A HREF = "velocity.html">velocity</A>
|
||||
or <A HREF = "set.html">set</A> command in the input script.
|
||||
0.0 when the <I>Atoms</I> section is read. Velocities can be set later by
|
||||
a <I>Velocities</I> section in the data file or by a
|
||||
<A HREF = "velocity.html">velocity</A> or <A HREF = "set.html">set</A> command in the input
|
||||
script.
|
||||
</P>
|
||||
<HR>
|
||||
|
||||
|
|
|
@ -227,7 +227,11 @@ line syntax: depends on atom style :ul
|
|||
|
||||
An {Atoms} section must appear in the data file if natoms > 0 in the
|
||||
header section. The atoms can be listed in any order. These are the
|
||||
line formats for each "atom style"_atom_style.html in LAMMPS:
|
||||
line formats for each "atom style"_atom_style.html in LAMMPS. As
|
||||
discussed below, each line can optionally have 3 flags (nx,ny,nz)
|
||||
appended to it, which indicate which image of a periodic simulation
|
||||
box the atom is in. These may be important to include for some kinds
|
||||
of analysis.
|
||||
|
||||
angle: atom-ID molecule-ID atom-type x y z
|
||||
atomic: atom-ID atom-type x y z
|
||||
|
@ -241,7 +245,7 @@ granular: atom-ID atom-type diameter density x y z
|
|||
molecular: atom-ID molecule-ID atom-type x y z
|
||||
hybrid: atom-ID atom-type x y z sub-style1 sub-style2 ... :tb(s=:)
|
||||
|
||||
where the keywords have these meanings:
|
||||
The keywords have these meanings:
|
||||
|
||||
atom-ID = integer ID of atom
|
||||
molecule-ID = integer ID of molecule the atom belongs to
|
||||
|
@ -304,20 +308,29 @@ were used in the input script, each atom line would have these fields:
|
|||
|
||||
atom-ID atom-type x y z q diameter density :pre
|
||||
|
||||
Atom lines (all lines or none of them) can optionally list 3 final
|
||||
Atom lines (all lines or none of them) can optionally list 3 trailing
|
||||
integer values: nx,ny,nz. For periodic dimensions, they specify which
|
||||
image of the box the atom is considered to be in. An image of 0 means
|
||||
the box as defined. A value of 2 means add 2 box lengths to get the
|
||||
true value. A value of -1 means subtract 1 box length to get the true
|
||||
value. LAMMPS updates these flags as atoms cross periodic boundaries
|
||||
during the simulation. The flags can be output with atom snapshots
|
||||
via the "dump"_dump.html command. If nx,ny,nz values are not set in
|
||||
the data file, LAMMPS initializes them to 0.
|
||||
it is inside the box as defined. A value of 2 means add 2 box lengths
|
||||
to get the true value. A value of -1 means subtract 1 box length to
|
||||
get the true value. LAMMPS updates these flags as atoms cross
|
||||
periodic boundaries during the simulation. The flags can be output
|
||||
with atom snapshots via the "dump"_dump.html command.
|
||||
|
||||
If nx,ny,nz values are not set in the data file, LAMMPS initializes
|
||||
them to 0. If image information is needed for later analysis and they
|
||||
are not all initially 0, it's important to set them correctly in the
|
||||
data file. Also, if you plan to use the "replicate"_replicate.html
|
||||
command to generate a larger system, these flags must be listed
|
||||
correctly for bonded atoms when the bond crosses a periodic boundary.
|
||||
I.e. the values of the image flags should be different by 1 (in the
|
||||
appropriate dimension) for the two atoms in such a bond.
|
||||
|
||||
Atom velocities and other atom quantities not defined above are set to
|
||||
0.0 when the {Atoms} section is read. They may later be set by a
|
||||
{Velocities} section in the data file or by a "velocity"_velocity.html
|
||||
or "set"_set.html command in the input script.
|
||||
0.0 when the {Atoms} section is read. Velocities can be set later by
|
||||
a {Velocities} section in the data file or by a
|
||||
"velocity"_velocity.html or "set"_set.html command in the input
|
||||
script.
|
||||
|
||||
:line
|
||||
|
||||
|
|
Loading…
Reference in New Issue