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2
doc/Section_commands.html
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@ -435,7 +435,7 @@ description:
<A HREF = "Section_start.html#2_3">LAMMPS is built with the appropriate package</A>.
</P>
<DIV ALIGN=center><TABLE BORDER=1 >
<TR ALIGN="center"><TD WIDTH="100"><A HREF = "ewald_n.html">ewald/n</A>
<TR ALIGN="center"><TD WIDTH="100"><A HREF = "kspace_style.html">ewald/n</A>
</TD></TR></TABLE></DIV>
</HTML>

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@ -110,7 +110,7 @@ request your input script and data files if necessary.
</P>
<HR>
<H4><A NAME = "9_3"></A>9.3 Error & warning Messages
<H4><A NAME = "9_3"></A>9.3 Error & warning messages
</H4>
<P>These are two alphabetic lists of the <A HREF = "#error">ERROR</A> and
<A HREF = "#warn">WARNING</A> messages LAMMPS prints out and the reason why. If the
@ -120,6 +120,11 @@ the error message and staring at the source code and comments is also
not a bad idea! Note that sometimes the same message can be printed
from multiple places in the code.
</P>
<P>Also note that error messages from <A HREF = "Section_start.html#2_3">user-contributed
packages</A> are not listed here. Is such an
error occurs and is not self-explanatory, you'll need to look in the
source code or contact the author of the package.
</P>
<H4><A NAME = "error"></A>Errors:
</H4>
<DL>

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@ -107,7 +107,7 @@ request your input script and data files if necessary.
:line
9.3 Error & warning Messages :h4,link(9_3)
9.3 Error & warning messages :h4,link(9_3)
These are two alphabetic lists of the "ERROR"_#error and
"WARNING"_#warn messages LAMMPS prints out and the reason why. If the
@ -117,6 +117,11 @@ the error message and staring at the source code and comments is also
not a bad idea! Note that sometimes the same message can be printed
from multiple places in the code.
Also note that error messages from "user-contributed
packages"_Section_start.html#2_3 are not listed here. Is such an
error occurs and is not self-explanatory, you'll need to look in the
source code or contact the author of the package.
Errors: :h4,link(error)
:dlb

95
doc/Section_modify.html
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@ -18,13 +18,19 @@ extend with new functionality. In fact, about 75% if its source code
is files added in this fashion.
</P>
<P>In this section, changes and additions users can make are listed along
with minimal instructions. The best way to add a new feature is to
find a similar feature in LAMMPS and look at the corresponding source
and header files to figure out what it does. You will need some
knowledge of C++ to be able to understand the hi-level structure of
LAMMPS and its class organization, but functions (class methods) that
do actual computations are written in vanilla C-style code and operate
on simple C-style data structures (vectors and arrays).
with minimal instructions. If you add a new feature to LAMMPS and
think it will be of interest to general users, we encourage you to
submit it to the developers for inclusion in the released version of
LAMMPS. Information about how to do this is provided
<A HREF = "#package">below</A>.
</P>
<P>The best way to add a new feature is to find a similar feature in
LAMMPS and look at the corresponding source and header files to figure
out what it does. You will need some knowledge of C++ to be able to
understand the hi-level structure of LAMMPS and its class
organization, but functions (class methods) that do actual
computations are written in vanilla C-style code and operate on simple
C-style data structures (vectors and arrays).
</P>
<P>Most of the new features described in this section require you to
write a new C++ derived class (except for exceptions described below,
@ -74,18 +80,25 @@ the executable and can be invoked with a pair_style command like the
example above. Arguments like 0.1 and 3.5 can be defined and
processed by your new class.
</P>
<P>Here is a list of the new features that can be added in this way:
<P>Here is a list of the new features that can be added in this way,
along with information about how to submit your features for inclusion
in the LAMMPS distribution.
</P>
<UL><LI><A HREF = "#atom">Atom styles</A>
<LI><A HREF = "#bond">Bond, angle, dihedral, improper potentials</A>
<LI><A HREF = "#compute">Compute styles</A>
<LI><A HREF = "#dump">Dump styles</A>
<LI><A HREF = "#dump">Dump custom output optoins</A>
<LI><A HREF = "#fix">Fix styles</A> which include integrators, temperature and pressure control, force constraints, boundary conditions, diagnostic output, etc
<LI><A HREF = "#command">Input script commands</A>
<LI><A HREF = "#kspace">Kspace computations</A>
<LI><A HREF = "#min">Minimization solvers</A>
<LI><A HREF = "#pair">Pairwise potentials</A>
<LI><A HREF = "#region">Region styles</A>
<LI><A HREF = "#region">Region styles</A>
<LI><A HREF = "#thermo">Thermodynamic output options</A>
<LI><A HREF = "#variable">Variable options</A>
</UL>
<UL><LI><A HREF = "#package">Submitting new features to the developers to include in LAMMPS</A>
</UL>
<P>As illustrated by the pairwise example, these options are referred to
in the LAMMPS documentation as the "style" of a particular command.
@ -513,6 +526,70 @@ then be accessed by variables) was discussed
</P>
<HR>
<A NAME = "package"></A><H4>Submitting new features to the developers to include in LAMMPS
</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.
</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
support your code which means answer questions, fix bugs, and maintain
it if LAMMPS changes.
</P>
<P>The previous sections of this doc page describe how to add new
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
developers</A>, since we may or may
not want to make those changes.
</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 of these details.
</P>
<P>Your user package will be a directory with a name like USER-FOO. In
addition to your new files, the directory should contain a README,
Install.csh and style_user_foo.h file.
</P>
<P>The README text file should contain your name and contact information
and a brief description of what your new package does. This is for
users to look at.
</P>
<P>The Install.csh and style_user_foo.h files enable 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, 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. Note that
the more clear and self-exaplantory you make your documentation, the
more likely it is that users will try out your new feature.
</P>
<HR>
<HR>
<A NAME = "Foo"></A>

95
doc/Section_modify.txt
View File

@ -15,13 +15,19 @@ extend with new functionality. In fact, about 75% if its source code
is files added in this fashion.
In this section, changes and additions users can make are listed along
with minimal instructions. The best way to add a new feature is to
find a similar feature in LAMMPS and look at the corresponding source
and header files to figure out what it does. You will need some
knowledge of C++ to be able to understand the hi-level structure of
LAMMPS and its class organization, but functions (class methods) that
do actual computations are written in vanilla C-style code and operate
on simple C-style data structures (vectors and arrays).
with minimal instructions. If you add a new feature to LAMMPS and
think it will be of interest to general users, we encourage you to
submit it to the developers for inclusion in the released version of
LAMMPS. Information about how to do this is provided
"below"_#package.
The best way to add a new feature is to find a similar feature in
LAMMPS and look at the corresponding source and header files to figure
out what it does. You will need some knowledge of C++ to be able to
understand the hi-level structure of LAMMPS and its class
organization, but functions (class methods) that do actual
computations are written in vanilla C-style code and operate on simple
C-style data structures (vectors and arrays).
Most of the new features described in this section require you to
write a new C++ derived class (except for exceptions described below,
@ -71,12 +77,15 @@ the executable and can be invoked with a pair_style command like the
example above. Arguments like 0.1 and 3.5 can be defined and
processed by your new class.
Here is a list of the new features that can be added in this way:
Here is a list of the new features that can be added in this way,
along with information about how to submit your features for inclusion
in the LAMMPS distribution.
"Atom styles"_#atom
"Bond, angle, dihedral, improper potentials"_#bond
"Compute styles"_#compute
"Dump styles"_#dump
"Dump custom output optoins"_#dump
"Fix styles"_#fix which include integrators, \
temperature and pressure control, force constraints, \
boundary conditions, diagnostic output, etc
@ -84,7 +93,11 @@ Here is a list of the new features that can be added in this way:
"Kspace computations"_#kspace
"Minimization solvers"_#min
"Pairwise potentials"_#pair
"Region styles"_#region :ul
"Region styles"_#region
"Thermodynamic output options"_#thermo
"Variable options"_#variable :ul
"Submitting new features to the developers to include in LAMMPS"_#package :ul
As illustrated by the pairwise example, these options are referred to
in the LAMMPS documentation as the "style" of a particular command.
@ -488,6 +501,70 @@ Adding new "compute styles"_compute.html (whose calculated values can
then be accessed by variables) was discussed
"here"_Section_modify.html#compute on this page.
:line
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.
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
support your code which means answer questions, fix bugs, and maintain
it if LAMMPS changes.
The previous sections of this doc page describe how to add new
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
developers"_http://lammps.sandia.gov/authors.html, since we may or may
not want to make those changes.
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 of these details.
Your user package will be a directory with a name like USER-FOO. In
addition to your new files, the directory should contain a README,
Install.csh and style_user_foo.h file.
The README text file should contain your name and contact information
and a brief description of what your new package does. This is for
users to look at.
The Install.csh and style_user_foo.h files enable LAMMPS to include
and exclude your package.
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.
Finally, 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. Note that
the more clear and self-exaplantory you make your documentation, the
more likely it is that users will try out your new feature.
:line
:line

61
doc/Section_start.html
View File

@ -269,11 +269,11 @@ instructions for tips. Good luck - we can't help you on this one.
<H4><A NAME = "2_3"></A>2.3 Making LAMMPS with optional packages
</H4>
<P>The source code for LAMMPS is structured as a large set of core files
that are always used plus additional optional packages, which are
groups of files that enable a specific set of features. For example,
force fields for molecular systems or granular systems are in
packages. You can see the list of both standard and user-contributed
packages by typing "make package".
which are always used, plus optional packages, which are groups of
files that enable a specific set of features. For example, force
fields for molecular systems or granular systems are in packages. You
can see the list of both standard and user-contributed packages by
typing "make package".
</P>
<P>The current list of standard packages is as follows:
</P>
@ -294,8 +294,8 @@ packages by typing "make package".
</TD></TR></TABLE></DIV>
<P>There are also user-contributed packages which may be as simple as a
single additional file (class) or many files grouped together which
add a specific functionality to the code. The difference between a
single additional file or many files grouped together which add a
specific functionality to the code. The difference between a
<I>standard</I> package versus a <I>user</I> package is as follows.
</P>
<P>Standard packages are supported by the LAMMPS developers and are
@ -305,49 +305,10 @@ necessary, and keep them compatible with future changes to LAMMPS.
</P>
<P>User packages don't necessarily meet these requirements. If you have
problems using a feature provided in a user package, you will likely
need to contact the contributor directly to get help.
</P>
<P>We encourage users to submit new features to <A HREF = "http://lammps.sandia.gov/authors.html">the
developers</A> that they add to
LAMMPS, especially if you think they will be useful to other users.
If they are broadly useful and meet the requirements listed above, we
may add them as core files to LAMMPS or as part of a standard package.
Else we will add them as a user package.
</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.
</P>
<P><A HREF = "Section_modify.html">This section</A> of the documentation describes how
to add new features of various kinds to LAMMPS. Packages are simply
collections of these kinds of new class files which are typically
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
requires something else in LAMMPS to change, you'll need to
<A HREF = "http://lammps.sandia.gov/authors.html">communicate with the
developers</A>.
</P>
<P>Examples of user-contributed packages are in src sub-directories that
start with USER. We impose only a few minor restrictions on the
source files you submit. They 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. You need to provide the Install.csh and
style*.h files that enable the package to be installed/un-installed.
See any of the other LAMMPS source or package files for examples.
Following this pattern will save you and us time when you submit the
files.
</P>
<P>Finally, you also need to include a README file with your package, so
that other users can get a quick idea of what it does and know how to
contact you. You also need to include a doc file in text format for
each of the new styles you are adding, which we will convert to HTML.
See the doc directory for numerous examples of these *.txt files; you
should use one of them as a template for the feature you are adding.
need to contact the contributor directly to get help. Information on
how to submit additions you make to LAMMPS as a user-contributed
package is given in <A HREF = "Section_modify.html#package">this section</A> of the
documentation.
</P>
<HR>

61
doc/Section_start.txt
View File

@ -264,11 +264,11 @@ instructions for tips. Good luck - we can't help you on this one.
2.3 Making LAMMPS with optional packages :h4,link(2_3)
The source code for LAMMPS is structured as a large set of core files
that are always used plus additional optional packages, which are
groups of files that enable a specific set of features. For example,
force fields for molecular systems or granular systems are in
packages. You can see the list of both standard and user-contributed
packages by typing "make package".
which are always used, plus optional packages, which are groups of
files that enable a specific set of features. For example, force
fields for molecular systems or granular systems are in packages. You
can see the list of both standard and user-contributed packages by
typing "make package".
The current list of standard packages is as follows:
@ -287,8 +287,8 @@ poems : coupled rigid body motion
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 (class) or many files grouped together which
add a specific functionality to the code. The difference between a
single additional file 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.
Standard packages are supported by the LAMMPS developers and are
@ -298,49 +298,10 @@ necessary, and keep them compatible with future changes to LAMMPS.
User packages don't necessarily meet these requirements. If you have
problems using a feature provided in a user package, you will likely
need to contact the contributor directly to get help.
We encourage users to submit new features to "the
developers"_http://lammps.sandia.gov/authors.html that they add to
LAMMPS, especially if you think they will be useful to other users.
If they are broadly useful and meet the requirements listed above, we
may add them as core files to LAMMPS or as part of a standard package.
Else we will add them as a user package.
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.
"This section"_Section_modify.html of the documentation describes how
to add new features of various kinds to LAMMPS. Packages are simply
collections of these kinds of new class files which are typically
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
requires something else in LAMMPS to change, you'll need to
"communicate with the
developers"_http://lammps.sandia.gov/authors.html.
Examples of user-contributed packages are in src sub-directories that
start with USER. We impose only a few minor restrictions on the
source files you submit. They 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. You need to provide the Install.csh and
style*.h files that enable the package to be installed/un-installed.
See any of the other LAMMPS source or package files for examples.
Following this pattern will save you and us time when you submit the
files.
Finally, you also need to include a README file with your package, so
that other users can get a quick idea of what it does and know how to
contact you. You also need to include a doc file in text format for
each of the new styles you are adding, which we will convert to HTML.
See the doc directory for numerous examples of these *.txt files; you
should use one of them as a template for the feature you are adding.
need to contact the contributor directly to get help. Information on
how to submit additions you make to LAMMPS as a user-contributed
package is given in "this section"_Section_modify.html#package of the
documentation.
:line

47
doc/kspace_style.html
View File

@ -15,7 +15,7 @@
</P>
<PRE>kspace_style style value
</PRE>
<UL><LI>style = <I>none</I> or <I>ewald</I> or <I>pppm</I> or others as referenced below
<UL><LI>style = <I>none</I> or <I>ewald</I> or <I>pppm</I> or <I>pppm/tip4p</I> or <I>ewald/n</I>
<PRE> <I>none</I> value = none
<I>ewald</I> value = precision
@ -23,6 +23,8 @@
<I>pppm</I> value = precision
precision = desired accuracy
<I>pppm/tip4p</I> value = precision
precision = desired accuracy
<I>ewald/n</I> value = precision
precision = desired accuracy
</PRE>
@ -34,12 +36,12 @@ kspace_style none
</PRE>
<P><B>Description:</B>
</P>
<P>Define a reciprocal (K-space) solver for LAMMPS to use each timestep
to compute long-range Coulombic interactions. When such a solver is
used in conjunction with an appropriate pair style, the cutoff for
Coulombic interactions is effectively infinite; each charge in the
system interacts with charges in an infinite array of periodic images
of the simulation domain.
<P>Define a K-space solver for LAMMPS to use each timestep to compute
long-range Coulombic interactions or long-range 1/r^N interactions.
When such a solver is used in conjunction with an appropriate pair
style, the cutoff for Coulombic or other 1/r^N interactions is
effectively infinite; each charge in the system interacts with charges
in an infinite array of periodic images of the simulation domain.
</P>
<P>The <I>ewald</I> style performs a standard Ewald summation as described in
any solid-state physics text.
@ -59,15 +61,21 @@ adds a charge at the massless 4th site in each TIP4P water molecule.
It should be used with <A HREF = "pair_style.html">pair styles</A> with a
<I>long/tip4p</I> in their style name.
</P>
<P>There are also additional kspace styles submitted by users which are
included in the LAMMPS distribution. The list of these with links to
the individual styles are given in the kspace section of <A HREF = "Section_commands.html#3_5">this
page</A>.
<P>The <I>ewald/n</I> style augments <I>ewald</I> by adding long-range dispersion
sum capabilities for 1/r^N potentials and is useful for simulation of
interfaces <A HREF = "#Veld">(Veld)</A>. It also performs standard coulombic Ewald
summations, but in a more efficient manner than the <I>ewald</I> style.
The 1/r^N capability means that Lennard-Jones or Buckingham potentials
can be used with <I>ewald/n</I> without a cutoff, i.e. they become full
long-range potentials.
</P>
<P>When a kspace style is used, a pair style that includes the
short-range correction to the pairwise Coulombic forces must also be
selected. These styles are ones that have a <I>coul/long</I> in their
style name.
short-range correction to the pairwise Coulombic or other 1/r^N forces
must also be selected. For Coulombic interactions, these styles are
ones that have a <I>coul/long</I> in their style name. For Lennard-Jones
or Buckingham interactions, see the <A HREF = "pair_lj_coul.html">pair_style
lj/coul</A> or <A HREF = "pair_buck_coul.html">pair_style
buck/coul</A> potentials.
</P>
<P>A precision value of 1.0e-4 means one part in 10000. This setting is
used in conjunction with the pairwise cutoff to determine the number
@ -85,13 +93,18 @@ must be periodic and the z dimension must be non-periodic.
if LAMMPS was built with that package. See the <A HREF = "Section_start.html#2_3">Making
LAMMPS</A> section for more info.
</P>
<P>The <I>ewald/n</I> style is part of the "user-ewaldn" package. It is only
enabled if LAMMPS was built with that package. See the <A HREF = "Section_start.html#2_3">Making
LAMMPS</A> section for more info.
</P>
<P>When using a long-range pairwise TIP4P potential, you must use kspace
style <I>pppm/tip4p</I> and vice versa.
</P>
<P><B>Related commands:</B>
</P>
<P><A HREF = "kspace_modify.html">kspace_modify</A>, <A HREF = "pair_style.html">pair_style</A>
lj/cut/coul/long, <A HREF = "pair_style.html">pair_style</A> lj/charmm/coul/long
lj/cut/coul/long, <A HREF = "pair_style.html">pair_style</A> lj/charmm/coul/long,
<A HREF = "pair_style">pair_style</A> lj/coul, <A HREF = "pair_style">pair_style</A> buck/coul
</P>
<P><B>Default:</B>
</P>
@ -112,4 +125,8 @@ Adam Hilger, NY (1989).
<P><B>(Pollock)</B> Pollock and Glosli, Comp Phys Comm, 95, 93 (1996).
</P>
<A NAME = "Veld"></A>
<P><B>(Veld)</B> In 't Veld, Ismail, Grest, J Chem Phys, in press (2007).
</P>
</HTML>

2
doc/shape.html
View File

@ -36,7 +36,7 @@ can also be set in the <A HREF = "read_data.html">read_data</A> data file. See
ellipsoid</A> require that shapes be set.
</P>
<P>Dipoles use the atom shape to compute a moment of inertia for
rotational energy. Only the 1st componenet of the shape is used since
rotational energy. Only the 1st component of the shape is used since
the particles are assumed to be spherical. The value of the first
component should be the same as the Lennard-Jones sigma value defined
in the dipole pair potential, i.e. in <A HREF = "pair_dipole.html">pair_style

2
doc/shape.txt
View File

@ -33,7 +33,7 @@ Currently, only "atom_style dipole"_atom_style.html and "atom_style
ellipsoid"_atom_style.html require that shapes be set.
Dipoles use the atom shape to compute a moment of inertia for
rotational energy. Only the 1st componenet of the shape is used since
rotational energy. Only the 1st component of the shape is used since
the particles are assumed to be spherical. The value of the first
component should be the same as the Lennard-Jones sigma value defined
in the dipole pair potential, i.e. in "pair_style