jianmu
/
lammps
forked from lijiext/lammps
1
0
Fork 0
Code Issues Pull Requests Packages Projects Releases Wiki Activity

git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@1246 f3b2605a-c512-4ea7-a41b-209d697bcdaa

This commit is contained in:
sjplimp 2007-12-11 23:28:43 +00:00
parent d33f6f99a3
commit c30a5382d8
2 changed files with 50 additions and 24 deletions
Show Stats Download Patch File Download Diff File Expand all files Collapse all files

37
doc/read_data.html
View File

@ -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>

37
doc/read_data.txt
View File

@ -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