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git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@6629 f3b2605a-c512-4ea7-a41b-209d697bcdaa

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sjplimp 2011-08-08 20:57:05 +00:00
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6 changed files with 130 additions and 98 deletions

108
doc/Section_modify.html
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@ -536,21 +536,23 @@ then be accessed by variables) was discussed
</H4>
<P>We encourage users to submit new features that they add to LAMMPS to
<A HREF = "http://lammps.sandia.gov/authors.html">the developers</A>, especially if
you think they will be useful to other users. If they are broadly
useful we may add them as core files to LAMMPS or as part of a
<A HREF = "Section_start.html#2_3">standard package</A>. Else we will add them as a
user-contributed package. Examples of user packages are in src
sub-directories that start with USER. You can see a list of the both
standard and user packages by typing "make package" in the LAMMPS src
directory.
you think the features will be of interest to other users. If they
are broadly useful we may add them as core files to LAMMPS or as part
of a <A HREF = "Section_start.html#2_3">standard package</A>. Else we will add them
as a user-contributed package or file. Examples of user packages are
in src sub-directories that start with USER. The USER-MISC package is
simply a collection of (mostly) unrelated single files, which is the
simplest way to have your contribution quickly added to the LAMMPS
distribution. You can see a list of the both standard and user
packages by typing "make package" in the LAMMPS src directory.
</P>
<P>With user packages, all we are really providing (aside from the fame
and fortune that accompanies having your name in the source code and
on the <A HREF = "http://lammps.sandia.gov/authors.html">Authors page</A> of the
<A HREF = "http://lammps.sandia.gov">LAMMPS WWW site</A>), is a means for you to distribute your work to
the LAMMPS user community and a mechanism for others to easily try out
your new feature. This may help you find bugs or make contact with
new collaborators. Note that you're also implicitly agreeing to
<P>With user packages and files, all we are really providing (aside from
the fame and fortune that accompanies having your name in the source
code and on the <A HREF = "http://lammps.sandia.gov/authors.html">Authors page</A>
of the <A HREF = "http://lammps.sandia.gov">LAMMPS WWW site</A>), is a means for you to distribute your
work to the LAMMPS user community and a mechanism for others to easily
try out your new feature. This may help you find bugs or make contact
with new collaborators. Note that you're also implicitly agreeing to
support your code which means answer questions, fix bugs, and maintain
it if LAMMPS changes.
</P>
@ -559,42 +561,56 @@ features of various kinds to LAMMPS. Packages are simply collections
of one or more new class files which are invoked as a new "style"
within a LAMMPS input script. If designed correctly, these additions
do not require changes to the main core of LAMMPS; they are simply
add-on files. If you think your new feature does requires changes in
other LAMMPS files, you'll need to <A HREF = "http://lammps.sandia.gov/authors.html">communicate with the
add-on files. If you think your new feature requires non-trivial
changes in core LAMMPS files, you'll need to <A HREF = "http://lammps.sandia.gov/authors.html">communicate with the
developers</A>, since we may or may
not want to make those changes.
not want to make those changes. An example of a trivial change is
making a parent-class method "virtual" when you derive a new child
class from it.
</P>
<P>Here is what you need to do to submit a user package for our
consideration. Following these steps will save time for both you and
us. See existing package files for examples.
<P>Here is what you need to do to submit a user package or single file
for our consideration. Following these steps will save time for both
you and us. See existing package files for examples.
</P>
<P>Your user package will be a directory with a name like USER-FOO. In
<UL><LI>All source files you provide must compile with the most current
version of LAMMPS.
<LI>If your contribution is a single file (actually a *.cpp and *.h file)
it can most rapidly be added to the USER-MISC directory. Send us the
one-line entry to add to the USER-MISC/README file in that dir, along
with the 2 source files. You can do this multiple times if you wish
to contribute several individual features.
<LI>If your contribution is several related featues, it is probably best
to make it a user package directory with a name like USER-FOO. In
addition to your new files, the directory should contain a README, and
Install.csh file. Send us a tarball of this USER-FOO directory.
</P>
<P>The README text file should contain your name and contact information
and a brief description of what your new package does.
</P>
<P>The Install.csh file enables LAMMPS to include and exclude your
package.
</P>
<P>Your new source files need to have the LAMMPS copyright, GPL notice,
and your name at the top. They need to create a class that is inside
the LAMMPS namespace. Other than that, your files can do whatever is
necessary to implement the new features. They don't have to be
written in the same style and syntax as other LAMMPS files, thought
that would be nice.
</P>
<P>Finally, in addition to the USER-FOO tarball, you also need to send us
a documentation file for each new command or style you are adding to
LAMMPS. These are text files which we will convert to HTML. Use one
of the *.txt files in the doc dir as a starting point for the new file
you create, since it should look similar to the doc files for existing
commands and styles. The "Restrictions" section of the doc page
should indicate that your feature is only available if LAMMPS is built
with the "user-foo" package. See other user package files for an
example of how to do this.
</P>
Install.csh file. The README text file should contain your name and
contact information and a brief description of what your new package
does. The Install.csh file enables LAMMPS to include and exclude your
package. See other README and Install.sh files in other USER
directories as examples. Send us a tarball of this USER-FOO
directory.
<LI>Your new source files need to have the LAMMPS copyright, GPL notice,
and your name at the top, like other LAMMPS source files. They need
to create a class that is inside the LAMMPS namespace. Other than
that, your files can do whatever is necessary to implement the new
features. They don't have to be written in the same stylistic format
and syntax as other LAMMPS files, though that would be nice.
<LI>Finally, you must also send a documentation file for each new command
or style you are adding to LAMMPS. This will be one file for a
single-file feature. For a package, it might be several files. These
are simple text files which we will convert to HTML. They must be in
the same format as other *.txt files in the lammps/doc directory for
similar commands and styles. The "Restrictions" section of the doc
page should indicate that your command is only available if LAMMPS is
built with the appropriate USER-MISC or USER-FOO package. See other
user package doc files for an example of how to do this. The txt2html
tool we use to do the conversion can be downloaded from <A HREF = "http://www.sandia.gov/~sjplimp/download.html">this
site</A>, so you can perform
the HTML conversion yourself to proofread your doc page.
</UL>
<P>Note that the more clear and self-explanatory you make your doc and
README files, the more likely it is that users will try out your new
feature.

100
doc/Section_modify.txt
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@ -513,21 +513,23 @@ Submitting new features to the developers to include in LAMMPS :link(package),h4
We encourage users to submit new features that they add to LAMMPS to
"the developers"_http://lammps.sandia.gov/authors.html, especially if
you think they will be useful to other users. If they are broadly
useful we may add them as core files to LAMMPS or as part of a
"standard package"_Section_start.html#2_3. Else we will add them as a
user-contributed package. Examples of user packages are in src
sub-directories that start with USER. You can see a list of the both
standard and user packages by typing "make package" in the LAMMPS src
directory.
you think the features will be of interest to other users. If they
are broadly useful we may add them as core files to LAMMPS or as part
of a "standard package"_Section_start.html#2_3. Else we will add them
as a user-contributed package or file. Examples of user packages are
in src sub-directories that start with USER. The USER-MISC package is
simply a collection of (mostly) unrelated single files, which is the
simplest way to have your contribution quickly added to the LAMMPS
distribution. You can see a list of the both standard and user
packages by typing "make package" in the LAMMPS src directory.
With user packages, all we are really providing (aside from the fame
and fortune that accompanies having your name in the source code and
on the "Authors page"_http://lammps.sandia.gov/authors.html of the
"LAMMPS WWW site"_lws), is a means for you to distribute your work to
the LAMMPS user community and a mechanism for others to easily try out
your new feature. This may help you find bugs or make contact with
new collaborators. Note that you're also implicitly agreeing to
With user packages and files, all we are really providing (aside from
the fame and fortune that accompanies having your name in the source
code and on the "Authors page"_http://lammps.sandia.gov/authors.html
of the "LAMMPS WWW site"_lws), is a means for you to distribute your
work to the LAMMPS user community and a mechanism for others to easily
try out your new feature. This may help you find bugs or make contact
with new collaborators. Note that you're also implicitly agreeing to
support your code which means answer questions, fix bugs, and maintain
it if LAMMPS changes.
@ -536,41 +538,55 @@ features of various kinds to LAMMPS. Packages are simply collections
of one or more new class files which are invoked as a new "style"
within a LAMMPS input script. If designed correctly, these additions
do not require changes to the main core of LAMMPS; they are simply
add-on files. If you think your new feature does requires changes in
other LAMMPS files, you'll need to "communicate with the
add-on files. If you think your new feature requires non-trivial
changes in core LAMMPS files, you'll need to "communicate with the
developers"_http://lammps.sandia.gov/authors.html, since we may or may
not want to make those changes.
not want to make those changes. An example of a trivial change is
making a parent-class method "virtual" when you derive a new child
class from it.
Here is what you need to do to submit a user package for our
consideration. Following these steps will save time for both you and
us. See existing package files for examples.
Here is what you need to do to submit a user package or single file
for our consideration. Following these steps will save time for both
you and us. See existing package files for examples.
Your user package will be a directory with a name like USER-FOO. In
All source files you provide must compile with the most current
version of LAMMPS. :ulb,l
If your contribution is a single file (actually a *.cpp and *.h file)
it can most rapidly be added to the USER-MISC directory. Send us the
one-line entry to add to the USER-MISC/README file in that dir, along
with the 2 source files. You can do this multiple times if you wish
to contribute several individual features. :l
If your contribution is several related featues, it is probably best
to make it a user package directory with a name like USER-FOO. In
addition to your new files, the directory should contain a README, and
Install.csh file. Send us a tarball of this USER-FOO directory.
The README text file should contain your name and contact information
and a brief description of what your new package does.
The Install.csh file enables LAMMPS to include and exclude your
package.
Install.csh file. The README text file should contain your name and
contact information and a brief description of what your new package
does. The Install.csh file enables LAMMPS to include and exclude your
package. See other README and Install.sh files in other USER
directories as examples. Send us a tarball of this USER-FOO
directory. :l
Your new source files need to have the LAMMPS copyright, GPL notice,
and your name at the top. They need to create a class that is inside
the LAMMPS namespace. Other than that, your files can do whatever is
necessary to implement the new features. They don't have to be
written in the same style and syntax as other LAMMPS files, thought
that would be nice.
and your name at the top, like other LAMMPS source files. They need
to create a class that is inside the LAMMPS namespace. Other than
that, your files can do whatever is necessary to implement the new
features. They don't have to be written in the same stylistic format
and syntax as other LAMMPS files, though that would be nice. :l
Finally, in addition to the USER-FOO tarball, you also need to send us
a documentation file for each new command or style you are adding to
LAMMPS. These are text files which we will convert to HTML. Use one
of the *.txt files in the doc dir as a starting point for the new file
you create, since it should look similar to the doc files for existing
commands and styles. The "Restrictions" section of the doc page
should indicate that your feature is only available if LAMMPS is built
with the "user-foo" package. See other user package files for an
example of how to do this.
Finally, you must also send a documentation file for each new command
or style you are adding to LAMMPS. This will be one file for a
single-file feature. For a package, it might be several files. These
are simple text files which we will convert to HTML. They must be in
the same format as other *.txt files in the lammps/doc directory for
similar commands and styles. The "Restrictions" section of the doc
page should indicate that your command is only available if LAMMPS is
built with the appropriate USER-MISC or USER-FOO package. See other
user package doc files for an example of how to do this. The txt2html
tool we use to do the conversion can be downloaded from "this
site"_http://www.sandia.gov/~sjplimp/download.html, so you can perform
the HTML conversion yourself to proofread your doc page. :l,ule
Note that the more clear and self-explanatory you make your doc and
README files, the more likely it is that users will try out your new

6
doc/Section_start.html
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@ -314,7 +314,7 @@ manually specify the correct -lsfftw or -ldfftw.
</P>
<P>(3.d) The FFT_INC variable also allows for a -DFFT_SINGLE setting that
will use single-precision FFTs with PPPM, which can speed-up
long-range calulations, particularly in parallel or on a GPU. Fourier
long-range calulations, particularly in parallel or on GPUs. Fourier
transform and related PPPM operations are somewhat insensitive to
floating point truncation errors and thus do not always need to be
performed in double precision. Using the -DFFT_SINGLE setting trades
@ -491,8 +491,8 @@ package".
</TD></TR></TABLE></DIV>
<P>There are also user-contributed packages which may be as simple as a
single additional file or many files grouped together which add a
specific functionality to the code.
single additional file (see the src/USER-MISC directory) or many files
grouped together which add a specific functionality to the code.
</P>
<P>The difference between a <I>standard</I> package versus a <I>user</I> package is
as follows.

6
doc/Section_start.txt
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@ -309,7 +309,7 @@ manually specify the correct -lsfftw or -ldfftw.
(3.d) The FFT_INC variable also allows for a -DFFT_SINGLE setting that
will use single-precision FFTs with PPPM, which can speed-up
long-range calulations, particularly in parallel or on a GPU. Fourier
long-range calulations, particularly in parallel or on GPUs. Fourier
transform and related PPPM operations are somewhat insensitive to
floating point truncation errors and thus do not always need to be
performed in double precision. Using the -DFFT_SINGLE setting trades
@ -484,8 +484,8 @@ srd : stochastic rotation dynamics (SRD)
xtc : dump atom snapshots in XTC format :tb(s=:)
There are also user-contributed packages which may be as simple as a
single additional file or many files grouped together which add a
specific functionality to the code.
single additional file (see the src/USER-MISC directory) or many files
grouped together which add a specific functionality to the code.
The difference between a {standard} package versus a {user} package is
as follows.

4
doc/kspace_style.html
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@ -89,8 +89,8 @@ using the compiler switch -DFFT_SINGLE for the FFT_INC setting in your
lo-level Makefile. This setting also changes some of the PPPM
operations (e.g. mapping charge to mesh and interpolating electric
fields to particles) to be performed in single precision. This option
can speed-up long-range calulations, particularly in parallel or on a
GPU. The use of the -DFFT_SINGLE flag is discussed in <A HREF = "Section_start.html#2_2_4">this
can speed-up long-range calulations, particularly in parallel or on
GPUs. The use of the -DFFT_SINGLE flag is discussed in <A HREF = "Section_start.html#2_2_4">this
section</A> of the manual.
</P>
<HR>

4
doc/kspace_style.txt
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@ -84,8 +84,8 @@ using the compiler switch -DFFT_SINGLE for the FFT_INC setting in your
lo-level Makefile. This setting also changes some of the PPPM
operations (e.g. mapping charge to mesh and interpolating electric
fields to particles) to be performed in single precision. This option
can speed-up long-range calulations, particularly in parallel or on a
GPU. The use of the -DFFT_SINGLE flag is discussed in "this
can speed-up long-range calulations, particularly in parallel or on
GPUs. The use of the -DFFT_SINGLE flag is discussed in "this
section"_Section_start.html#2_2_4 of the manual.
:line