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14
doc/Manual.html
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@ -24,21 +24,19 @@ National Laboratories, a US Department of Energy facility, with
funding from the DOE. It is an open-source code, distributed freely
under the terms of the GNU Public License (GPL).
</P>
<P>The primary author of the code is <A HREF = "http://www.cs.sandia.gov/~sjplimp">Steve Plimpton</A>, who can be
contacted at <A HREF = "mailto:sjplimp@sandia.gov">sjplimp@sandia.gov</A>. The <A HREF = "http://lammps.sandia.gov">LAMMPS WWW Site</A> at
www.cs.sandia.gov/~sjplimp/lammps.html has more information about the
code and its uses.
<P>The developers of LAMMPS are <A HREF = "http://www.cs.sandia.gov/~sjplimp">Steve Plimpton</A>, Paul Crozier, and
Aidan Thompson who can be contacted at "sjplimp, pscrozi, athomps at
sandia.gov. The <A HREF = "http://lammps.sandia.gov">LAMMPS WWW Site</A> at http://lammps.sandia.gov has
more information about the code and its uses.
</P>
<HR>
<P>The LAMMPS documentation is organized into the following sections. If
you find errors or omissions in this manual or have suggestions for
useful information to add, please send us an <A HREF = "mailto:sjplimp@sandia.gov">email</A> so we can
improve the LAMMPS documentation.
useful information to add, please send an email to the developers so
we can improve the LAMMPS documentation.
</P>
<P><A HREF = "Manual.pdf">PDF file</A> of the entire manual, generated by
<A HREF = "http://www.easysw.com/htmldoc">htmldoc</A>

13
doc/Manual.txt
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@ -21,20 +21,19 @@ National Laboratories, a US Department of Energy facility, with
funding from the DOE. It is an open-source code, distributed freely
under the terms of the GNU Public License (GPL).
The primary author of the code is "Steve Plimpton"_sjp, who can be
contacted at "sjplimp@sandia.gov"_mail. The "LAMMPS WWW Site"_lws at
www.cs.sandia.gov/~sjplimp/lammps.html has more information about the
code and its uses.
The developers of LAMMPS are "Steve Plimpton"_sjp, Paul Crozier, and
Aidan Thompson who can be contacted at "sjplimp, pscrozi, athomps at
sandia.gov. The "LAMMPS WWW Site"_lws at http://lammps.sandia.gov has
more information about the code and its uses.
:link(sjp,http://www.cs.sandia.gov/~sjplimp)
:link(mail,mailto:sjplimp@sandia.gov)
:line
The LAMMPS documentation is organized into the following sections. If
you find errors or omissions in this manual or have suggestions for
useful information to add, please send us an "email"_mail so we can
improve the LAMMPS documentation.
useful information to add, please send an email to the developers so
we can improve the LAMMPS documentation.
"PDF file"_Manual.pdf of the entire manual, generated by
"htmldoc"_http://www.easysw.com/htmldoc

6
doc/Section_errors.html
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@ -47,10 +47,8 @@ you can fix the problem. Of course LAMMPS cannot figure out your
physics mistakes, like choosing too big a timestep, specifying invalid
force field coefficients, or putting 2 atoms on top of each other! If
you find errors that LAMMPS doesn't catch that you think it should
flag, please send us an <A HREF = "mailto:sjplimp@sandia.gov">email</A>.
flag, please send an email to the developers.
</P>
<P>If you get an error message about an invalid command in your input
script, you can determine what command is causing the problem by
looking in the log.lammps file or using the <A HREF = "echo.html">echo command</A>
@ -94,7 +92,7 @@ buffering or boost the sizes of messages that can be buffered.
<A NAME = "9_2"></A><H4>9.2 Reporting bugs
</H4>
<P>If you are confident that you have found a bug in LAMMPS, we'd like to
know about it via <A HREF = "mailto:sjplimp@sandia.gov">email</A>.
know about it via <A HREF = "mail">email</A>.
</P>
<P>First, check the "New features and bug fixes" section of the <A HREF = "http://lammps.sandia.gov">LAMMPS
WWW site</A> to see if the bug has already been reported or fixed.

4
doc/Section_errors.txt
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@ -44,9 +44,7 @@ you can fix the problem. Of course LAMMPS cannot figure out your
physics mistakes, like choosing too big a timestep, specifying invalid
force field coefficients, or putting 2 atoms on top of each other! If
you find errors that LAMMPS doesn't catch that you think it should
flag, please send us an "email"_mail.
:link(mail,mailto:sjplimp@sandia.gov)
flag, please send an email to the developers.
If you get an error message about an invalid command in your input
script, you can determine what command is causing the problem by

23
doc/Section_intro.html
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@ -339,11 +339,9 @@ source file headers (including the copyright and GPL notices) should
remain part of the code.
</P>
<P>In the spirit of an open-source code, these are various ways you can
contribute to making LAMMPS better. You can send <A HREF = "mailto:sjplimp@sandia.gov">email</A> on any
of these items.
contribute to making LAMMPS better. You can send email to the
developers on any of these items.
</P>
<UL><LI>Point prospective users to the <A HREF = "http://lammps.sandia.gov">LAMMPS WWW Site</A>. Mention it in
talks or link to it from your WWW site.
@ -384,7 +382,7 @@ added to the page.
Site</A>. It might be added to the page. No promises.
<LI>Cash. Small denominations, unmarked bills preferred. Paper sack OK.
Leave on desk. <A HREF = "mailto:sjplimp@sandia.gov">VISA</A> also accepted. Chocolate chip cookies
Leave on desk. <A HREF = "email">VISA</A> also accepted. Chocolate chip cookies
encouraged.
</UL>
<HR>
@ -423,17 +421,20 @@ Computing, Minneapolis, MN (March 1997).
</P>
<P>If you use LAMMPS results in your published work, please cite the J
Comp Phys reference and include a pointer to the <A HREF = "http://lammps.sandia.gov">LAMMPS WWW Site</A>
(www.cs.sandia.gov/~sjplimp/lammps.html). A paper describing the
latest version of LAMMPS is in the works; when it appears in print,
you can check the <A HREF = "http://lammps.sandia.gov">LAMMPS WWW Site</A> for a more current citation.
(http://lammps.sandia.gov). A paper describing the latest version of
LAMMPS is in the works; when it appears in print, you can check the
<A HREF = "http://lammps.sandia.gov">LAMMPS WWW Site</A> for a more current citation.
</P>
<P>If you send me information about your publication, I'll be pleased to
add it to the Publications page of the <A HREF = "http://lammps.sandia.gov">LAMMPS WWW Site</A>. Ditto
for a picture or movie for the Pictures or Movies pages.
</P>
<P>The primary author of LAMMPS is <A HREF = "http://www.cs.sandia.gov/~sjplimp">Steve Plimpton</A> at Sandia
National Labs. Others have made significant contributions to the
code:
<P>The core group of LAMMPS developers are at Sandia National Labs. They
include <A HREF = "http://www.cs.sandia.gov/~sjplimp">Steve Plimpton</A>, Paul Crozier, and Aidan Thompson and can
be contacted via email: sjplimp, pscrozi, athomps at sandia.gov.
</P>
<P>Here are various folks who have made significant contributions to
features in LAMMPS:
</P>

21
doc/Section_intro.txt
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@ -327,10 +327,8 @@ source file headers (including the copyright and GPL notices) should
remain part of the code.
In the spirit of an open-source code, these are various ways you can
contribute to making LAMMPS better. You can send "email"_email on any
of these items.
:link(email,mailto:sjplimp@sandia.gov)
contribute to making LAMMPS better. You can send email to the
developers on any of these items.
Point prospective users to the "LAMMPS WWW Site"_lws. Mention it in
talks or link to it from your WWW site. :ulb,l
@ -407,17 +405,20 @@ Computing, Minneapolis, MN (March 1997).
If you use LAMMPS results in your published work, please cite the J
Comp Phys reference and include a pointer to the "LAMMPS WWW Site"_lws
(www.cs.sandia.gov/~sjplimp/lammps.html). A paper describing the
latest version of LAMMPS is in the works; when it appears in print,
you can check the "LAMMPS WWW Site"_lws for a more current citation.
(http://lammps.sandia.gov). A paper describing the latest version of
LAMMPS is in the works; when it appears in print, you can check the
"LAMMPS WWW Site"_lws for a more current citation.
If you send me information about your publication, I'll be pleased to
add it to the Publications page of the "LAMMPS WWW Site"_lws. Ditto
for a picture or movie for the Pictures or Movies pages.
The primary author of LAMMPS is "Steve Plimpton"_sjp at Sandia
National Labs. Others have made significant contributions to the
code:
The core group of LAMMPS developers are at Sandia National Labs. They
include "Steve Plimpton"_sjp, Paul Crozier, and Aidan Thompson and can
be contacted via email: sjplimp, pscrozi, athomps at sandia.gov.
Here are various folks who have made significant contributions to
features in LAMMPS:
:link(sjp,http://www.cs.sandia.gov/~sjplimp)

7
doc/Section_modify.html
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@ -119,11 +119,10 @@ follow the unit conventions discussed by the <A HREF = "units.html">units</A>
command.
</P>
<P>If you add something you think is truly useful and doesn't impact
LAMMPS performance when it isn't used, send me an <A HREF = "mailto:sjplimp@sandia.gov">email</A>. We
might be interested in adding it to the LAMMPS distribution.
LAMMPS performance when it isn't used, send an email to the
developers. We might be interested in adding it to the LAMMPS
distribution.
</P>
<HR>
<A NAME = "pair"></A><H4>Pairwise potentials

7
doc/Section_modify.txt
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@ -118,10 +118,9 @@ follow the unit conventions discussed by the "units"_units.html
command.
If you add something you think is truly useful and doesn't impact
LAMMPS performance when it isn't used, send me an "email"_mail. We
might be interested in adding it to the LAMMPS distribution.
:link(mail,mailto:sjplimp@sandia.gov)
LAMMPS performance when it isn't used, send an email to the
developers. We might be interested in adding it to the LAMMPS
distribution.
:line

13
doc/Section_start.html
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@ -57,22 +57,19 @@ makefile, there are compiler options, additional libraries can be used
(MPI, FFT), etc. Please read this section carefully. If you are not
comfortable with makefiles, or building codes on a Unix platform, or
running an MPI job on your machine, please find a local expert to help
you. Many of the emails I get about build and run problems are not
you. Many of the emails we get about build and run problems are not
really about LAMMPS - they are peculiar to the user's system,
compilers, libraries, etc. Such questions are better answered by a
local expert.
</P>
<P>If you have a build problem that you are convinced is a LAMMPS issue
(e.g. the compiler complains about a line of LAMMPS source code), then
please send an <A HREF = "mailto:sjplimp@sandia.gov">email</A>. Note that doesn't include linking
problems - that's a question for a local expert!
please send an email to the developers. Note that doesn't include
linking problems - that's a question for a local expert!
</P>
<P>Also, if you succeed in building LAMMPS on a new kind of machine
(which there isn't a similar Makefile for in the distribution), send
it to sjplimp@sandia.gov and we'll include it in future LAMMPS
releases.
it to the developers and we'll include it in future LAMMPS releases.
</P>
<P><B><I>Building a LAMMPS executable:</I></B>
</P>
@ -179,7 +176,7 @@ you'll need to set the appropriate -I and -L switches in Makefile.foo.
<P>If you examine fft3d.c and fft3d.h you'll see it's possible to add
other vendor FFT libraries via #ifdef statements in the appropriate
places. If you successfully add a new FFT option, like -DFFT_IBM,
please send me an email; I'd like to add it to LAMMPS.
please send the developers an email; we'd like to add it to LAMMPS.
</P>
<P>(6) If you don't plan to use PPPM, you don't need an FFT library. Use
a -DFFT_NONE switch in the CCFLAGS setting of Makefile.foo, or exclude

13
doc/Section_start.txt
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@ -52,22 +52,19 @@ makefile, there are compiler options, additional libraries can be used
(MPI, FFT), etc. Please read this section carefully. If you are not
comfortable with makefiles, or building codes on a Unix platform, or
running an MPI job on your machine, please find a local expert to help
you. Many of the emails I get about build and run problems are not
you. Many of the emails we get about build and run problems are not
really about LAMMPS - they are peculiar to the user's system,
compilers, libraries, etc. Such questions are better answered by a
local expert.
If you have a build problem that you are convinced is a LAMMPS issue
(e.g. the compiler complains about a line of LAMMPS source code), then
please send an "email"_mail. Note that doesn't include linking
problems - that's a question for a local expert!
:link(mail,mailto:sjplimp@sandia.gov)
please send an email to the developers. Note that doesn't include
linking problems - that's a question for a local expert!
Also, if you succeed in building LAMMPS on a new kind of machine
(which there isn't a similar Makefile for in the distribution), send
it to sjplimp@sandia.gov and we'll include it in future LAMMPS
releases.
it to the developers and we'll include it in future LAMMPS releases.
[{Building a LAMMPS executable:}]
@ -174,7 +171,7 @@ you'll need to set the appropriate -I and -L switches in Makefile.foo.
If you examine fft3d.c and fft3d.h you'll see it's possible to add
other vendor FFT libraries via #ifdef statements in the appropriate
places. If you successfully add a new FFT option, like -DFFT_IBM,
please send me an email; I'd like to add it to LAMMPS.
please send the developers an email; we'd like to add it to LAMMPS.
(6) If you don't plan to use PPPM, you don't need an FFT library. Use
a -DFFT_NONE switch in the CCFLAGS setting of Makefile.foo, or exclude

12
doc/pair_style_hybrid.html
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@ -56,6 +56,18 @@ atoms in the simulation will have both EAM and charge attributes.
</P>
<P><B>Restrictions:</B> none
</P>
<P>When using a long-range Coulomic solver (via the
<A HREF = "kspace_style">kspace_style</A> command) with pair_style hybrid, one or
more sub-styles will be of the "long" variety.
E.g. <I>lj/cut/coul/long</I> or <I>buck/coul/long</I>. It is OK to have more
than one sub-style with a "long" component, but you must insure that
the short-range Coulombic cutoff used by each of these pair styles is
consistent. Else the long-range Coulombic solve will be inconsistent.
</P>
<P>The hybrid style cannot include any of the <I>granular</I> styles in its
list of styles to use. Only one <I>coul/long</I> style can be used in the
list of hybrid styles.
</P>
<P><B>Related commands:</B>
</P>
<P><A HREF = "pair_coeff.html">pair_coeff</A>