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git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@11025 f3b2605a-c512-4ea7-a41b-209d697bcdaa

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sjplimp
2013-11-20 15:14:48 +00:00
parent 7162cf032d
commit cd11570fed
8 changed files with 47 additions and 41 deletions
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21
doc/dump.html
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@ -109,8 +109,8 @@ timesteps in one of several styles. The <I>image</I> style is the
exception; it creates a JPG or PPM image file of the atom
configuration every N timesteps, as discussed on the <A HREF = "dump_image.html">dump
image</A> doc page. The timesteps on which dump output
is written can also be controlled by a variable. See the <A HREF = "dump_modify.html">dump_modify
every</A> command.
is written can also be controlled by a variable; see the <A HREF = "dump_modify.html">dump_modify
every</A> command for details.
</P>
<P>Only information for atoms in the specified group is dumped. The
<A HREF = "dump_modify.html">dump_modify thresh and region</A> commands can also
@ -119,7 +119,7 @@ options; see details below.
</P>
<P>As described below, the filename determines the kind of output (text
or binary or gzipped, one big file or one per timestep, one big file
or one per processor).
or multiple smaller files).
</P>
<P>IMPORTANT NOTE: Because periodic boundary conditions are enforced only
on timesteps when neighbor lists are rebuilt, the coordinates of an
@ -134,7 +134,7 @@ if the <A HREF = "atom_modify.html">atom_modify sort</A> option is on, which it
by default. In this case atoms are re-ordered periodically during a
simulation, due to spatial sorting. It is also true when running in
parallel, because data for a single snapshot is collected from
multiple processors.
multiple processors, each of which owns a subset of the atoms.
</P>
<P>For the <I>atom</I>, <I>custom</I>, <I>cfg</I>, and <I>local</I> styles, sorting is off by
default. For the <I>dcd</I>, <I>xtc</I>, <I>xyz</I>, and <I>molfile</I> styles, sorting by
@ -293,11 +293,12 @@ from using the (numerical) atom type to an element name (or some
other label). This will help many visualization programs to guess
bonds and colors.
</P>
<P>Note that <I>atom</I>, <I>custom</I>, <I>dcd</I>, <I>xtc</I>, and <I>xyz</I> style dump files can
be read directly by <A HREF = "http://www.ks.uiuc.edu/Research/vmd">VMD</A> (a popular
molecular viewing program). See <A HREF = "Section_tools.html#vmd">Section tools</A>
of the manual and the tools/lmp2vmd/README.txt file for more information
about support in VMD for reading and visualizing LAMMPS dump files.
<P>Note that <I>atom</I>, <I>custom</I>, <I>dcd</I>, <I>xtc</I>, and <I>xyz</I> style dump files
can be read directly by <A HREF = "http://www.ks.uiuc.edu/Research/vmd">VMD</A>, a
popular molecular viewing program. See <A HREF = "Section_tools.html#vmd">Section
tools</A> of the manual and the
tools/lmp2vmd/README.txt file for more information about support in
VMD for reading and visualizing LAMMPS dump files.
</P>
<HR>
@ -330,7 +331,7 @@ tmp.dump.20000, etc. This option is not available for the <I>dcd</I> and
<I>xtc</I> styles. Note that the <A HREF = "dump_modify.html">dump_modify pad</A>
command can be used to insure all timestep numbers are the same length
(e.g. 00010), which can make it easier to read a series of dump files
in order by some post-processing tools.
in order with some post-processing tools.
</P>
<P>If a "%" character appears in the filename, then each of P processors
writes a portion of the dump file, and the "%" character is replaced

21
doc/dump.txt
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@ -97,8 +97,8 @@ timesteps in one of several styles. The {image} style is the
exception; it creates a JPG or PPM image file of the atom
configuration every N timesteps, as discussed on the "dump
image"_dump_image.html doc page. The timesteps on which dump output
is written can also be controlled by a variable. See the "dump_modify
every"_dump_modify.html command.
is written can also be controlled by a variable; see the "dump_modify
every"_dump_modify.html command for details.
Only information for atoms in the specified group is dumped. The
"dump_modify thresh and region"_dump_modify.html commands can also
@ -107,7 +107,7 @@ options; see details below.
As described below, the filename determines the kind of output (text
or binary or gzipped, one big file or one per timestep, one big file
or one per processor).
or multiple smaller files).
IMPORTANT NOTE: Because periodic boundary conditions are enforced only
on timesteps when neighbor lists are rebuilt, the coordinates of an
@ -122,7 +122,7 @@ if the "atom_modify sort"_atom_modify.html option is on, which it is
by default. In this case atoms are re-ordered periodically during a
simulation, due to spatial sorting. It is also true when running in
parallel, because data for a single snapshot is collected from
multiple processors.
multiple processors, each of which owns a subset of the atoms.
For the {atom}, {custom}, {cfg}, and {local} styles, sorting is off by
default. For the {dcd}, {xtc}, {xyz}, and {molfile} styles, sorting by
@ -281,11 +281,12 @@ from using the (numerical) atom type to an element name (or some
other label). This will help many visualization programs to guess
bonds and colors.
Note that {atom}, {custom}, {dcd}, {xtc}, and {xyz} style dump files can
be read directly by "VMD"_http://www.ks.uiuc.edu/Research/vmd (a popular
molecular viewing program). See "Section tools"_Section_tools.html#vmd
of the manual and the tools/lmp2vmd/README.txt file for more information
about support in VMD for reading and visualizing LAMMPS dump files.
Note that {atom}, {custom}, {dcd}, {xtc}, and {xyz} style dump files
can be read directly by "VMD"_http://www.ks.uiuc.edu/Research/vmd, a
popular molecular viewing program. See "Section
tools"_Section_tools.html#vmd of the manual and the
tools/lmp2vmd/README.txt file for more information about support in
VMD for reading and visualizing LAMMPS dump files.
:line
@ -318,7 +319,7 @@ tmp.dump.20000, etc. This option is not available for the {dcd} and
{xtc} styles. Note that the "dump_modify pad"_dump_modify.html
command can be used to insure all timestep numbers are the same length
(e.g. 00010), which can make it easier to read a series of dump files
in order by some post-processing tools.
in order with some post-processing tools.
If a "%" character appears in the filename, then each of P processors
writes a portion of the dump file, and the "%" character is replaced

8
doc/dump_modify.html
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@ -100,9 +100,9 @@
<I>color</I> args = name R G B
name = name of color
R,G,B = red/green/blue numeric values from 0.0 to 1.0
</PRE>
<I>framerate</I> arg = fps
fps = frames per second for movie
</PRE>
</UL>
<P><B>Examples:</B>
@ -245,6 +245,8 @@ the first two fields (atom id and type) are not actually written into
the CFG file, though you must include formats for them in the format
string.
</P>
<HR>
<P>The <I>fileper</I> keyword is documented below with the <I>nfile</I> keyword.
</P>
<HR>
@ -262,7 +264,7 @@ attributes in the dump command itself.
<HR>
<P>The <I>label</I> keyword applies only to the dump <I>local</I> style. When
it writes local informatoin, such as bond or angle topology
it writes local information, such as bond or angle topology
to a dump file, it will use the specified <I>label</I> to format
the header. By default this includes 2 lines:
</P>
@ -359,7 +361,7 @@ cost, as well as memory, versus unsorted output.
<HR>
<P>The <I>thresh</I> keyword only applies to the dump <I>custom</I>, <I>cfg</I>,
<I>image</I>, and <I>mvoie</I> styles. Multiple thresholds can be specified.
<I>image</I>, and <I>movie</I> styles. Multiple thresholds can be specified.
Specifying "none" turns off all threshold criteria. If thresholds are
specified, only atoms whose attributes meet all the threshold criteria
are written to the dump file or included in the image. The possible

10
doc/dump_modify.txt
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@ -89,9 +89,9 @@ keyword = {acolor} or {adiam} or {amap} or {bcolor} or {bdiam} or {backcolor} or
color = name of color for box lines
{color} args = name R G B
name = name of color
R,G,B = red/green/blue numeric values from 0.0 to 1.0 :pre
R,G,B = red/green/blue numeric values from 0.0 to 1.0
{framerate} arg = fps
fps = frames per second for movie
fps = frames per second for movie :pre
:ule
[Examples:]
@ -233,6 +233,8 @@ the first two fields (atom id and type) are not actually written into
the CFG file, though you must include formats for them in the format
string.
:line
The {fileper} keyword is documented below with the {nfile} keyword.
:line
@ -250,7 +252,7 @@ attributes in the dump command itself.
:line
The {label} keyword applies only to the dump {local} style. When
it writes local informatoin, such as bond or angle topology
it writes local information, such as bond or angle topology
to a dump file, it will use the specified {label} to format
the header. By default this includes 2 lines:
@ -347,7 +349,7 @@ cost, as well as memory, versus unsorted output.
:line
The {thresh} keyword only applies to the dump {custom}, {cfg},
{image}, and {mvoie} styles. Multiple thresholds can be specified.
{image}, and {movie} styles. Multiple thresholds can be specified.
Specifying "none" turns off all threshold criteria. If thresholds are
specified, only atoms whose attributes meet all the threshold criteria
are written to the dump file or included in the image. The possible

8
doc/neb.html
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@ -71,11 +71,11 @@ for further discussion.
there to be one processor per replica.
</P>
<P>IMPORTANT NOTE: As explained below, a NEB calculation perfoms a
damped-dynamics minimization across all the replicas. This uses
damped-dynamics minimization across all the replicas. This will use
whatever timestep you have defined in your input script, via the
<A HREF = "timestep.html">timestep</A> command. You may get faster convergence if
you use a larger timestep than you would normally use for dynamics
with the same system.
<A HREF = "timestep.html">timestep</A> command. You may get faster convergence for
a NEB calculation if you use a larger timestep than you would normally
use for dynamics with the same system.
</P>
<P>When a NEB calculation is performed, it is assumed that each replica
is running the same system, though LAMMPS does not check for this.

8
doc/neb.txt
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@ -61,11 +61,11 @@ IMPORTANT NOTE: The current NEB implementation in LAMMPS only allows
there to be one processor per replica.
IMPORTANT NOTE: As explained below, a NEB calculation perfoms a
damped-dynamics minimization across all the replicas. This uses
damped-dynamics minimization across all the replicas. This will use
whatever timestep you have defined in your input script, via the
"timestep"_timestep.html command. You may get faster convergence if
you use a larger timestep than you would normally use for dynamics
with the same system.
"timestep"_timestep.html command. You may get faster convergence for
a NEB calculation if you use a larger timestep than you would normally
use for dynamics with the same system.
When a NEB calculation is performed, it is assumed that each replica
is running the same system, though LAMMPS does not check for this.

4
doc/variable.html
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@ -418,8 +418,8 @@ would occur with the default precedence.
<P>IMPORTANT NOTE: Because a unary minus is higher precedence than
exponentiation, the formula "-2^2" will evaluate to 4, not -4. This
convention is compatible with some programming languages, but not
others. This behavior can be overridden with parenthesis; the formula
"-(2^2)" will evaluate to -4.
others. As mentioned, this behavior can be easily overridden with
parenthesis; the formula "-(2^2)" will evaluate to -4.
</P>
<P>The 6 relational operators return either a 1.0 or 0.0 depending on
whether the relationship between x and y is TRUE or FALSE. For

4
doc/variable.txt
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@ -418,8 +418,8 @@ would occur with the default precedence.
IMPORTANT NOTE: Because a unary minus is higher precedence than
exponentiation, the formula "-2^2" will evaluate to 4, not -4. This
convention is compatible with some programming languages, but not
others. This behavior can be overridden with parenthesis; the formula
"-(2^2)" will evaluate to -4.
others. As mentioned, this behavior can be easily overridden with
parenthesis; the formula "-(2^2)" will evaluate to -4.
The 6 relational operators return either a 1.0 or 0.0 depending on
whether the relationship between x and y is TRUE or FALSE. For