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git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@946 f3b2605a-c512-4ea7-a41b-209d697bcdaa

This commit is contained in:
sjplimp 2007-10-04 00:21:14 +00:00
parent 67d45d04f5
commit 54856bbbea
48 changed files with 356 additions and 117 deletions
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2
doc/Section_modify.html
View File

@ -560,7 +560,7 @@ 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.
us. See existing package files for examples.
</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,

2
doc/Section_modify.txt
View File

@ -537,7 +537,7 @@ 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.
us. See existing package files for examples.
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,

9
doc/pair_airebo.html
View File

@ -106,8 +106,8 @@ off.
</P>
<HR>
<P><B>Mixing, shift, table, tail correction, per-atom energy/stress, and
restart info</B>:
<P><B>Mixing, shift, table, tail correction, per-atom energy/stress,
restart, and rRESPA info</B>:
</P>
<P>This pair style does not support the <A HREF = "pair_modify.html">pair_modify</A>
mix, shift, table, and tail options.
@ -122,6 +122,11 @@ files</A>, since it is stored in potential files. Thus, you
need to re-specify the pair_style and pair_coeff commands in an input
script that reads a restart file.
</P>
<P>This pair style can only be used via the <I>pair</I> keyword of the
<A HREF = "run_style.html">run_style respa</A> command. It does not support the
<I>inner</I>, <I>middle</I>, <I>outer</I> keywords of the <A HREF = "run_style.html">run_style
command</A>.
</P>
<P><B>Restrictions:</B>
</P>
<P>This pair style is part of the "manybody" package. It is only enabled

9
doc/pair_airebo.txt
View File

@ -103,8 +103,8 @@ off.
:line
[Mixing, shift, table, tail correction, per-atom energy/stress, and
restart info]:
[Mixing, shift, table, tail correction, per-atom energy/stress,
restart, and rRESPA info]:
This pair style does not support the "pair_modify"_pair_modify.html
mix, shift, table, and tail options.
@ -119,6 +119,11 @@ files"_restart.html, since it is stored in potential files. Thus, you
need to re-specify the pair_style and pair_coeff commands in an input
script that reads a restart file.
This pair style can only be used via the {pair} keyword of the
"run_style respa"_run_style.html command. It does not support the
{inner}, {middle}, {outer} keywords of the "run_style
command"_run_style.html.
[Restrictions:]
This pair style is part of the "manybody" package. It is only enabled

13
doc/pair_buck.html
View File

@ -72,6 +72,8 @@ commands:
<LI>cutoff (distance units)
<LI>cutoff2 (distance units)
</UL>
<P>The second coefficient, rho, must be greater than zero.
</P>
<P>The latter 2 coefficients are optional. If not specified, the global
LJ and Coulombic cutoffs are used. If only one cutoff is specified,
it is used as the cutoff for both LJ and Coulombic interactions for
@ -79,8 +81,6 @@ this type pair. If both coefficients are specified, they are used as
the LJ and Coulombic cutoffs for this type pair. You cannot specify 2
cutoffs for style <I>buck</I>, since it has no Coulombic terms.
</P>
<P>The second coefficient, rho, must be greater than zero.
</P>
<P>For <I>buck/coul/long</I> only the LJ cutoff can be specified since a
Coulombic cutoff cannot be specified for an individual I,J type pair.
All type pairs use the same global Coulombic cutoff specified in the
@ -106,15 +106,20 @@ capability has not yet been added to this potential.
<A HREF = "pair_modify.html">pair_modify</A> tail option for adding long-range tail
corrections to energy and pressure.
</P>
<P>All of the Buckinham pair styles can calculate per-atom energy and
<P>All of the Buckingham pair styles can calculate per-atom energy and
stress, as used by the <A HREF = "compute_epair_atom.html">compute epair/atom</A>,
<A HREF = "compute_stress_atom.html">compute stress/atom</A>, and <A HREF = "dump.html">dump
custom</A> commands.
</P>
<P>All of the Buckinham pair styles write their information to <A HREF = "restart.html">binary
<P>All of the Buckingham pair styles write their information to <A HREF = "restart.html">binary
restart files</A>, so pair_style and pair_coeff commands do
not need to be specified in an input script that reads a restart file.
</P>
<P>All of the Buckingham pair styles can only be used via the <I>pair</I>
keyword of the <A HREF = "run_style.html">run_style respa</A> command. They do not
support the <I>inner</I>, <I>middle</I>, <I>outer</I> keywords of the <A HREF = "run_style.html">run_style
command</A>.
</P>
<P><B>Restrictions:</B>
</P>
<P>The <I>buck/coul/long</I> style is part of the "kspace" package. It is

13
doc/pair_buck.txt
View File

@ -66,6 +66,8 @@ C (energy-distance^6 units)
cutoff (distance units)
cutoff2 (distance units) :ul
The second coefficient, rho, must be greater than zero.
The latter 2 coefficients are optional. If not specified, the global
LJ and Coulombic cutoffs are used. If only one cutoff is specified,
it is used as the cutoff for both LJ and Coulombic interactions for
@ -73,8 +75,6 @@ this type pair. If both coefficients are specified, they are used as
the LJ and Coulombic cutoffs for this type pair. You cannot specify 2
cutoffs for style {buck}, since it has no Coulombic terms.
The second coefficient, rho, must be greater than zero.
For {buck/coul/long} only the LJ cutoff can be specified since a
Coulombic cutoff cannot be specified for an individual I,J type pair.
All type pairs use the same global Coulombic cutoff specified in the
@ -100,15 +100,20 @@ None of the Buckingham pair styles support the
"pair_modify"_pair_modify.html tail option for adding long-range tail
corrections to energy and pressure.
All of the Buckinham pair styles can calculate per-atom energy and
All of the Buckingham pair styles can calculate per-atom energy and
stress, as used by the "compute epair/atom"_compute_epair_atom.html,
"compute stress/atom"_compute_stress_atom.html, and "dump
custom"_dump.html commands.
All of the Buckinham pair styles write their information to "binary
All of the Buckingham pair styles write their information to "binary
restart files"_restart.html, so pair_style and pair_coeff commands do
not need to be specified in an input script that reads a restart file.
All of the Buckingham pair styles can only be used via the {pair}
keyword of the "run_style respa"_run_style.html command. They do not
support the {inner}, {middle}, {outer} keywords of the "run_style
command"_run_style.html.
[Restrictions:]
The {buck/coul/long} style is part of the "kspace" package. It is

11
doc/pair_charmm.html
View File

@ -115,8 +115,8 @@ the pair_style command.
</P>
<HR>
<P><B>Mixing, shift, table, tail correction, per-atom energy/stress, and
restart info</B>:
<P><B>Mixing, shift, table, tail correction, per-atom energy/stress,
restart, and rRESPA info</B>:
</P>
<P>For atom type pairs I,J and I != J, the epsilon, sigma, epsilon_14,
and sigma_14 coefficients for all of the lj/charmm pair styles can be
@ -146,6 +146,13 @@ custom</A> commands.
restart files</A>, so pair_style and pair_coeff commands do
not need to be specified in an input script that reads a restart file.
</P>
<P>The lj/charmm/coul/long pair style supports the use of the <I>inner</I>,
<I>middle</I>, and <I>outer</I> keywords of the <A HREF = "run_style.html">run_style respa</A>
command, meaning the pairwise forces can be partitioned by distance at
different levels of the rRESPA hierarchy. The other styles only
support the <I>pair</I> keyword of run_style respa. See the
<A HREF = "run_style.html">run_style</A> command for details.
</P>
<HR>
<P><B>Restrictions:</B>

11
doc/pair_charmm.txt
View File

@ -108,8 +108,8 @@ the pair_style command.
:line
[Mixing, shift, table, tail correction, per-atom energy/stress, and
restart info]:
[Mixing, shift, table, tail correction, per-atom energy/stress,
restart, and rRESPA info]:
For atom type pairs I,J and I != J, the epsilon, sigma, epsilon_14,
and sigma_14 coefficients for all of the lj/charmm pair styles can be
@ -139,6 +139,13 @@ All of the lj/charmm pair styles write their information to "binary
restart files"_restart.html, so pair_style and pair_coeff commands do
not need to be specified in an input script that reads a restart file.
The lj/charmm/coul/long pair style supports the use of the {inner},
{middle}, and {outer} keywords of the "run_style respa"_run_style.html
command, meaning the pairwise forces can be partitioned by distance at
different levels of the rRESPA hierarchy. The other styles only
support the {pair} keyword of run_style respa. See the
"run_style"_run_style.html command for details.
:line
[Restrictions:]

9
doc/pair_class2.html
View File

@ -96,8 +96,8 @@ mix</A> setting is thus ignored for class2 potentials
for epsilon and sigma. However it is still followed for mixing the
cutoff distance.
</P>
<P><B>Mixing, shift, table, tail correction, per-atom energy/stress, and
restart info</B>:
<P><B>Mixing, shift, table, tail correction, per-atom energy/stress,
restart, and rRESPA info</B>:
</P>
<P>For atom type pairs I,J and I != J, the epsilon and sigma coefficients
and cutoff distance for all of the lj/class2 pair styles can be mixed.
@ -128,6 +128,11 @@ custom</A> commands.
restart files</A>, so pair_style and pair_coeff commands do
not need to be specified in an input script that reads a restart file.
</P>
<P>All of the lj/class2 pair styles can only be used via the <I>pair</I>
keyword of the <A HREF = "run_style.html">run_style respa</A> command. They do not
support the <I>inner</I>, <I>middle</I>, <I>outer</I> keywords of the <A HREF = "run_style.html">run_style
command</A>.
</P>
<P><B>Restrictions:</B>
</P>
<P>All of these pair styles are part of the "class2" package. They are

9
doc/pair_class2.txt
View File

@ -90,8 +90,8 @@ mix"_pair_modify.html setting is thus ignored for class2 potentials
for epsilon and sigma. However it is still followed for mixing the
cutoff distance.
[Mixing, shift, table, tail correction, per-atom energy/stress, and
restart info]:
[Mixing, shift, table, tail correction, per-atom energy/stress,
restart, and rRESPA info]:
For atom type pairs I,J and I != J, the epsilon and sigma coefficients
and cutoff distance for all of the lj/class2 pair styles can be mixed.
@ -122,6 +122,11 @@ All of the lj/class2 pair styles write their information to "binary
restart files"_restart.html, so pair_style and pair_coeff commands do
not need to be specified in an input script that reads a restart file.
All of the lj/class2 pair styles can only be used via the {pair}
keyword of the "run_style respa"_run_style.html command. They do not
support the {inner}, {middle}, {outer} keywords of the "run_style
command"_run_style.html.
[Restrictions:]
All of these pair styles are part of the "class2" package. They are

9
doc/pair_colloid.html
View File

@ -112,8 +112,8 @@ colloid-solvent cutoff in this case.
</P>
<HR>
<P><B>Mixing, shift, table, tail correction, per-atom energy/stress, and
restart info</B>:
<P><B>Mixing, shift, table, tail correction, per-atom energy/stress,
restart, rRESPA info</B>:
</P>
<P>For atom type pairs I,J and I != J, the A, sigma, d1, and d2
coefficients and cutoff distance for this pair style can be mixed. A
@ -140,6 +140,11 @@ commands.
files</A>, so pair_style and pair_coeff commands do not need
to be specified in an input script that reads a restart file.
</P>
<P>This pair style can only be used via the <I>pair</I> keyword of the
<A HREF = "run_style.html">run_style respa</A> command. It does not support the
<I>inner</I>, <I>middle</I>, <I>outer</I> keywords of the <A HREF = "run_style.html">run_style
command</A>.
</P>
<HR>
<P><B>Restrictions:</B>

9
doc/pair_colloid.txt
View File

@ -109,8 +109,8 @@ colloid-solvent cutoff in this case.
:line
[Mixing, shift, table, tail correction, per-atom energy/stress, and
restart info]:
[Mixing, shift, table, tail correction, per-atom energy/stress,
restart, rRESPA info]:
For atom type pairs I,J and I != J, the A, sigma, d1, and d2
coefficients and cutoff distance for this pair style can be mixed. A
@ -137,6 +137,11 @@ This pair style writes its information to "binary restart
files"_restart.html, so pair_style and pair_coeff commands do not need
to be specified in an input script that reads a restart file.
This pair style can only be used via the {pair} keyword of the
"run_style respa"_run_style.html command. It does not support the
{inner}, {middle}, {outer} keywords of the "run_style
command"_run_style.html.
:line
[Restrictions:]

9
doc/pair_coul.html
View File

@ -73,8 +73,8 @@ Coulombic cutoff specified in the pair_style command.
</P>
<HR>
<P><B>Mixing, shift, table, tail correction, per-atom energy/stress, and
restart info</B>:
<P><B>Mixing, shift, table, tail correction, per-atom energy/stress,
restart, rRESPA info</B>:
</P>
<P>For atom type pairs I,J and I != J, the cutoff distance for the
<I>coul/cut</I> style can be mixed. The default mix value is <I>geometric</I>.
@ -100,6 +100,11 @@ commands.
files</A>, so pair_style and pair_coeff commands do not need
to be specified in an input script that reads a restart file.
</P>
<P>This pair style can only be used via the <I>pair</I> keyword of the
<A HREF = "run_style.html">run_style respa</A> command. It does not support the
<I>inner</I>, <I>middle</I>, <I>outer</I> keywords of the <A HREF = "run_style.html">run_style
command</A>.
</P>
<HR>
<P><B>Restrictions:</B>

9
doc/pair_coul.txt
View File

@ -69,8 +69,8 @@ Coulombic cutoff specified in the pair_style command.
:line
[Mixing, shift, table, tail correction, per-atom energy/stress, and
restart info]:
[Mixing, shift, table, tail correction, per-atom energy/stress,
restart, rRESPA info]:
For atom type pairs I,J and I != J, the cutoff distance for the
{coul/cut} style can be mixed. The default mix value is {geometric}.
@ -96,6 +96,11 @@ These pair styles write their information to "binary restart
files"_restart.html, so pair_style and pair_coeff commands do not need
to be specified in an input script that reads a restart file.
This pair style can only be used via the {pair} keyword of the
"run_style respa"_run_style.html command. It does not support the
{inner}, {middle}, {outer} keywords of the "run_style
command"_run_style.html.
:line
[Restrictions:]

9
doc/pair_dipole.html
View File

@ -78,8 +78,8 @@ type pair.
</P>
<HR>
<P><B>Mixing, shift, table, tail correction, per-atom energy/stress, and
restart info</B>:
<P><B>Mixing, shift, table, tail correction, per-atom energy/stress,
restart, rRESPA info</B>:
</P>
<P>For atom type pairs I,J and I != J, the epsilon and sigma coefficients
and cutoff distances for this pair style can be mixed. The default
@ -111,6 +111,11 @@ commands.
files</A>, so pair_style and pair_coeff commands do not need
to be specified in an input script that reads a restart file.
</P>
<P>This pair style can only be used via the <I>pair</I> keyword of the
<A HREF = "run_style.html">run_style respa</A> command. It does not support the
<I>inner</I>, <I>middle</I>, <I>outer</I> keywords of the <A HREF = "run_style.html">run_style
command</A>.
</P>
<P><B>Restrictions:</B>
</P>
<P>This style is part of the "dipole" package. It is only enabled if

9
doc/pair_dipole.txt
View File

@ -75,8 +75,8 @@ type pair.
:line
[Mixing, shift, table, tail correction, per-atom energy/stress, and
restart info]:
[Mixing, shift, table, tail correction, per-atom energy/stress,
restart, rRESPA info]:
For atom type pairs I,J and I != J, the epsilon and sigma coefficients
and cutoff distances for this pair style can be mixed. The default
@ -108,6 +108,11 @@ This pair style writes its information to "binary restart
files"_restart.html, so pair_style and pair_coeff commands do not need
to be specified in an input script that reads a restart file.
This pair style can only be used via the {pair} keyword of the
"run_style respa"_run_style.html command. It does not support the
{inner}, {middle}, {outer} keywords of the "run_style
command"_run_style.html.
[Restrictions:]
This style is part of the "dipole" package. It is only enabled if

9
doc/pair_dpd.html
View File

@ -58,8 +58,8 @@ command so it does not need to be specified.
</P>
<HR>
<P><B>Mixing, shift, table, tail correction, per-atom energy/stress, and
restart info</B>:
<P><B>Mixing, shift, table, tail correction, per-atom energy/stress,
restart, rRESPA info</B>:
</P>
<P>Thsi pair style does not support mixing. Thus, coefficients for all
I,J pairs must be specified explicitly.
@ -91,6 +91,11 @@ intially. This means the random forces will be random, but will not
be the same as they would have been if the original simulation had
continued past the restart time.
</P>
<P>This pair style can only be used via the <I>pair</I> keyword of the
<A HREF = "run_style.html">run_style respa</A> command. It does not support the
<I>inner</I>, <I>middle</I>, <I>outer</I> keywords of the <A HREF = "run_style.html">run_style
command</A>.
</P>
<HR>
<P><B>Restrictions:</B>

9
doc/pair_dpd.txt
View File

@ -55,8 +55,8 @@ command so it does not need to be specified.
:line
[Mixing, shift, table, tail correction, per-atom energy/stress, and
restart info]:
[Mixing, shift, table, tail correction, per-atom energy/stress,
restart, rRESPA info]:
Thsi pair style does not support mixing. Thus, coefficients for all
I,J pairs must be specified explicitly.
@ -88,6 +88,11 @@ intially. This means the random forces will be random, but will not
be the same as they would have been if the original simulation had
continued past the restart time.
This pair style can only be used via the {pair} keyword of the
"run_style respa"_run_style.html command. It does not support the
{inner}, {middle}, {outer} keywords of the "run_style
command"_run_style.html.
:line
[Restrictions:]

9
doc/pair_eam.html
View File

@ -322,8 +322,8 @@ are listed.
</P>
<HR>
<P><B>Mixing, shift, table, tail correction, per-atom energy/stress, and
restart info</B>:
<P><B>Mixing, shift, table, tail correction, per-atom energy/stress,
restart, rRESPA info</B>:
</P>
<P>For atom type pairs I,J and I != J, where types I and J correspond to
two different element types, mixing is performed by LAMMPS as
@ -344,6 +344,11 @@ files</A>, since it is stored in potential files. Thus, you
need to re-specify the pair_style and pair_coeff commands in an input
script that reads a restart file.
</P>
<P>The eam pair styles can only be used via the <I>pair</I> keyword of the
<A HREF = "run_style.html">run_style respa</A> command. They do not support the
<I>inner</I>, <I>middle</I>, <I>outer</I> keywords of the <A HREF = "run_style.html">run_style
command</A>.
</P>
<HR>
<P><B>Restrictions:</B>

9
doc/pair_eam.txt
View File

@ -314,8 +314,8 @@ are listed.
:line
[Mixing, shift, table, tail correction, per-atom energy/stress, and
restart info]:
[Mixing, shift, table, tail correction, per-atom energy/stress,
restart, rRESPA info]:
For atom type pairs I,J and I != J, where types I and J correspond to
two different element types, mixing is performed by LAMMPS as
@ -336,6 +336,11 @@ files"_restart.html, since it is stored in potential files. Thus, you
need to re-specify the pair_style and pair_coeff commands in an input
script that reads a restart file.
The eam pair styles can only be used via the {pair} keyword of the
"run_style respa"_run_style.html command. They do not support the
{inner}, {middle}, {outer} keywords of the "run_style
command"_run_style.html.
:line
[Restrictions:]

9
doc/pair_gayberne.html
View File

@ -117,8 +117,8 @@ to specify its interaction with other spherical particles.
</P>
<HR>
<P><B>Mixing, shift, table, tail correction, per-atom energy/stress, and
restart info</B>:
<P><B>Mixing, shift, table, tail correction, per-atom energy/stress,
restart, rRESPA info</B>:
</P>
<P>For atom type pairs I,J and I != J, the epsilon and sigma coefficients
and cutoff distance for this pair style can be mixed. The default mix
@ -146,6 +146,11 @@ commands.
files</A>, so pair_style and pair_coeff commands do not need
to be specified in an input script that reads a restart file.
</P>
<P>This pair style can only be used via the <I>pair</I> keyword of the
<A HREF = "run_style.html">run_style respa</A> command. It does not support the
<I>inner</I>, <I>middle</I>, <I>outer</I> keywords of the <A HREF = "run_style.html">run_style
command</A>.
</P>
<HR>
<P><B>Restrictions:</B>

9
doc/pair_gayberne.txt
View File

@ -114,8 +114,8 @@ to specify its interaction with other spherical particles.
:line
[Mixing, shift, table, tail correction, per-atom energy/stress, and
restart info]:
[Mixing, shift, table, tail correction, per-atom energy/stress,
restart, rRESPA info]:
For atom type pairs I,J and I != J, the epsilon and sigma coefficients
and cutoff distance for this pair style can be mixed. The default mix
@ -143,6 +143,11 @@ This pair style writes its information to "binary restart
files"_restart.html, so pair_style and pair_coeff commands do not need
to be specified in an input script that reads a restart file.
This pair style can only be used via the {pair} keyword of the
"run_style respa"_run_style.html command. It does not support the
{inner}, {middle}, {outer} keywords of the "run_style
command"_run_style.html.
:line
[Restrictions:]

15
doc/pair_gran.html
View File

@ -74,21 +74,26 @@ global settings are made via the pair_style command.
</P>
<HR>
<P><B>Mixing, shift, table, tail correction, per-atom energy/stress, and
restart info</B>:
<P><B>Mixing, shift, table, tail correction, per-atom energy/stress,
restart, rRESPA info</B>:
</P>
<P>The <A HREF = "pair_modify.html">pair_modify</A> mix, shift, table, and tail options
are not relevant for granular pair styles.
</P>
<P>This pair style does not calculate per-atom energy and stress, as used
<P>These pair styles do not calculate per-atom energy and stress, as used
by the <A HREF = "compute_epair_atom.html">compute epair/atom</A>, <A HREF = "compute_stress_atom.html">compute
stress/atom</A>, and <A HREF = "dump.html">dump custom</A>
commands.
</P>
<P>This pair style writes its information to <A HREF = "restart.html">binary restart
files</A>, so a pair_style commands does not need to be
<P>These pair styles write their information to <A HREF = "restart.html">binary restart
files</A>, so a pair_style command does not need to be
specified in an input script that reads a restart file.
</P>
<P>These pair styles can only be used via the <I>pair</I> keyword of the
<A HREF = "run_style.html">run_style respa</A> command. They do not support the
<I>inner</I>, <I>middle</I>, <I>outer</I> keywords of the <A HREF = "run_style.html">run_style
command</A>.
</P>
<HR>
<P><B>Restrictions:</B> none

15
doc/pair_gran.txt
View File

@ -65,21 +65,26 @@ See the citation below for more discussion of granular potentials.
:line
[Mixing, shift, table, tail correction, per-atom energy/stress, and
restart info]:
[Mixing, shift, table, tail correction, per-atom energy/stress,
restart, rRESPA info]:
The "pair_modify"_pair_modify.html mix, shift, table, and tail options
are not relevant for granular pair styles.
This pair style does not calculate per-atom energy and stress, as used
These pair styles do not calculate per-atom energy and stress, as used
by the "compute epair/atom"_compute_epair_atom.html, "compute
stress/atom"_compute_stress_atom.html, and "dump custom"_dump.html
commands.
This pair style writes its information to "binary restart
files"_restart.html, so a pair_style commands does not need to be
These pair styles write their information to "binary restart
files"_restart.html, so a pair_style command does not need to be
specified in an input script that reads a restart file.
These pair styles can only be used via the {pair} keyword of the
"run_style respa"_run_style.html command. They do not support the
{inner}, {middle}, {outer} keywords of the "run_style
command"_run_style.html.
:line
[Restrictions:] none

9
doc/pair_hybrid.html
View File

@ -124,8 +124,8 @@ potentials.
</P>
<HR>
<P><B>Mixing, shift, table, tail correction, per-atom energy/stress, and
restart info</B>:
<P><B>Mixing, shift, table, tail correction, per-atom energy/stress,
restart, rRESPA info</B>:
</P>
<P>Any pair potential settings made via the
<A HREF = "pair_modify.html">pair_modify</A> command are passed along to all
@ -158,6 +158,11 @@ specified in an input script that reads a restart file. However, the
coefficient information is not stored in the restart file. Thus,
pair_coeff commands need to be specified in the restart input script.
</P>
<P>These pair style can only be used via the <I>pair</I> keyword of the
<A HREF = "run_style.html">run_style respa</A> command. They do not support the
<I>inner</I>, <I>middle</I>, <I>outer</I> keywords of the <A HREF = "run_style.html">run_style
command</A>, even if their sub-styles do.
</P>
<P><B>Restrictions:</B>
</P>
<P>When using a long-range Coulomic solver (via the

9
doc/pair_hybrid.txt
View File

@ -120,8 +120,8 @@ potentials.
:line
[Mixing, shift, table, tail correction, per-atom energy/stress, and
restart info]:
[Mixing, shift, table, tail correction, per-atom energy/stress,
restart, rRESPA info]:
Any pair potential settings made via the
"pair_modify"_pair_modify.html command are passed along to all
@ -154,6 +154,11 @@ specified in an input script that reads a restart file. However, the
coefficient information is not stored in the restart file. Thus,
pair_coeff commands need to be specified in the restart input script.
These pair style can only be used via the {pair} keyword of the
"run_style respa"_run_style.html command. They do not support the
{inner}, {middle}, {outer} keywords of the "run_style
command"_run_style.html, even if their sub-styles do.
[Restrictions:]
When using a long-range Coulomic solver (via the

13
doc/pair_lj.html
View File

@ -80,7 +80,7 @@ pair_coeff 1 1 100.0 3.5 9.0
</PRE>
<P><B>Description:</B>
</P>
<P>The <I>lj/cut</I> styles compute the standard 6/12 Lennard-Jones potential,
<P>The <I>lj/cut</I> styles compute the standard 12/6 Lennard-Jones potential,
given by
</P>
<CENTER><IMG SRC = "Eqs/pair_lj.jpg">
@ -165,8 +165,8 @@ Coulombic cutoff specified in the pair_style command.
</P>
<HR>
<P><B>Mixing, shift, table, tail correction, per-atom energy/stress, and
restart info</B>:
<P><B>Mixing, shift, table, tail correction, per-atom energy/stress,
restart, and rRESPA info</B>:
</P>
<P>For atom type pairs I,J and I != J, the epsilon and sigma coefficients
and cutoff distance for all of the lj/cut pair styles can be mixed.
@ -196,6 +196,13 @@ custom</A> commands.
restart files</A>, so pair_style and pair_coeff commands do
not need to be specified in an input script that reads a restart file.
</P>
<P>The lj/cut and lj/cut/coul/long pair styles support the use of the
<I>inner</I>, <I>middle</I>, and <I>outer</I> keywords of the <A HREF = "run_style.html">run_style
respa</A> command, meaning the pairwise forces can be
partitioned by distance at different levels of the rRESPA hierarchy.
The other styles only support the <I>pair</I> keyword of run_style respa.
See the <A HREF = "run_style.html">run_style</A> command for details.
</P>
<HR>
<P><B>Restrictions:</B>

13
doc/pair_lj.txt
View File

@ -72,7 +72,7 @@ pair_coeff 1 1 100.0 3.5 9.0 :pre
[Description:]
The {lj/cut} styles compute the standard 6/12 Lennard-Jones potential,
The {lj/cut} styles compute the standard 12/6 Lennard-Jones potential,
given by
:c,image(Eqs/pair_lj.jpg)
@ -157,8 +157,8 @@ Coulombic cutoff specified in the pair_style command.
:line
[Mixing, shift, table, tail correction, per-atom energy/stress, and
restart info]:
[Mixing, shift, table, tail correction, per-atom energy/stress,
restart, and rRESPA info]:
For atom type pairs I,J and I != J, the epsilon and sigma coefficients
and cutoff distance for all of the lj/cut pair styles can be mixed.
@ -188,6 +188,13 @@ All of the lj/cut pair styles write their information to "binary
restart files"_restart.html, so pair_style and pair_coeff commands do
not need to be specified in an input script that reads a restart file.
The lj/cut and lj/cut/coul/long pair styles support the use of the
{inner}, {middle}, and {outer} keywords of the "run_style
respa"_run_style.html command, meaning the pairwise forces can be
partitioned by distance at different levels of the rRESPA hierarchy.
The other styles only support the {pair} keyword of run_style respa.
See the "run_style"_run_style.html command for details.
:line
[Restrictions:]

9
doc/pair_lj_expand.html
View File

@ -51,8 +51,8 @@ optional. If not specified, the global LJ cutoff is used.
</P>
<HR>
<P><B>Mixing, shift, table, tail correction, per-atom energy/stress, and
restart info</B>:
<P><B>Mixing, shift, table, tail correction, per-atom energy/stress,
restart, rRESPA info</B>:
</P>
<P>For atom type pairs I,J and I != J, the epsilon, sigma, and shift
coefficients and cutoff distance for this pair style can be mixed.
@ -80,6 +80,11 @@ commands.
files</A>, so pair_style and pair_coeff commands do not need
to be specified in an input script that reads a restart file.
</P>
<P>This pair style can only be used via the <I>pair</I> keyword of the
<A HREF = "run_style.html">run_style respa</A> command. It does not support the
<I>inner</I>, <I>middle</I>, <I>outer</I> keywords of the <A HREF = "run_style.html">run_style
command</A>.
</P>
<HR>
<P><B>Restrictions:</B> none

9
doc/pair_lj_expand.txt
View File

@ -48,8 +48,8 @@ optional. If not specified, the global LJ cutoff is used.
:line
[Mixing, shift, table, tail correction, per-atom energy/stress, and
restart info]:
[Mixing, shift, table, tail correction, per-atom energy/stress,
restart, rRESPA info]:
For atom type pairs I,J and I != J, the epsilon, sigma, and shift
coefficients and cutoff distance for this pair style can be mixed.
@ -77,6 +77,11 @@ This pair style writes its information to "binary restart
files"_restart.html, so pair_style and pair_coeff commands do not need
to be specified in an input script that reads a restart file.
This pair style can only be used via the {pair} keyword of the
"run_style respa"_run_style.html command. It does not support the
{inner}, {middle}, {outer} keywords of the "run_style
command"_run_style.html.
:line
[Restrictions:] none

9
doc/pair_lj_smooth.html
View File

@ -60,8 +60,8 @@ formula is used.
</P>
<HR>
<P><B>Mixing, shift, table, tail correction, per-atom energy/stress, and
restart info</B>:
<P><B>Mixing, shift, table, tail correction, per-atom energy/stress,
restart, rRESPA info</B>:
</P>
<P>For atom type pairs I,J and I != J, the epsilon, sigma, Rin
coefficients and the cutoff distance for this pair style can be mixed.
@ -90,6 +90,11 @@ commands.
files</A>, so pair_style and pair_coeff commands do not need
to be specified in an input script that reads a restart file.
</P>
<P>This pair style can only be used via the <I>pair</I> keyword of the
<A HREF = "run_style.html">run_style respa</A> command. It does not support the
<I>inner</I>, <I>middle</I>, <I>outer</I> keywords of the <A HREF = "run_style.html">run_style
command</A>.
</P>
<HR>
<P><B>Restrictions:</B> none

10
doc/pair_lj_smooth.txt
View File

@ -57,8 +57,8 @@ formula is used.
:line
[Mixing, shift, table, tail correction, per-atom energy/stress, and
restart info]:
[Mixing, shift, table, tail correction, per-atom energy/stress,
restart, rRESPA info]:
For atom type pairs I,J and I != J, the epsilon, sigma, Rin
coefficients and the cutoff distance for this pair style can be mixed.
@ -87,8 +87,12 @@ This pair style writes its information to "binary restart
files"_restart.html, so pair_style and pair_coeff commands do not need
to be specified in an input script that reads a restart file.
:line
This pair style can only be used via the {pair} keyword of the
"run_style respa"_run_style.html command. It does not support the
{inner}, {middle}, {outer} keywords of the "run_style
command"_run_style.html.
:line
[Restrictions:] none

9
doc/pair_meam.html
View File

@ -187,8 +187,8 @@ alloy interaction between elements 1 and 2 to 4.37.
</P>
<HR>
<P><B>Mixing, shift, table, tail correction, per-atom energy/stress, and
restart info</B>:
<P><B>Mixing, shift, table, tail correction, per-atom energy/stress,
restart, rRESPA info</B>:
</P>
<P>For atom type pairs I,J and I != J, where types I and J correspond to
two different element types, mixing is performed by LAMMPS with
@ -208,6 +208,11 @@ files</A>, since it is stored in potential files. Thus, you
need to re-specify the pair_style and pair_coeff commands in an input
script that reads a restart file.
</P>
<P>This pair style can only be used via the <I>pair</I> keyword of the
<A HREF = "run_style.html">run_style respa</A> command. It does not support the
<I>inner</I>, <I>middle</I>, <I>outer</I> keywords of the <A HREF = "run_style.html">run_style
command</A>.
</P>
<HR>
<P><B>Restrictions:</B>

9
doc/pair_meam.txt
View File

@ -184,8 +184,8 @@ alloy interaction between elements 1 and 2 to 4.37.
:line
[Mixing, shift, table, tail correction, per-atom energy/stress, and
restart info]:
[Mixing, shift, table, tail correction, per-atom energy/stress,
restart, rRESPA info]:
For atom type pairs I,J and I != J, where types I and J correspond to
two different element types, mixing is performed by LAMMPS with
@ -205,6 +205,11 @@ files"_restart.html, since it is stored in potential files. Thus, you
need to re-specify the pair_style and pair_coeff commands in an input
script that reads a restart file.
This pair style can only be used via the {pair} keyword of the
"run_style respa"_run_style.html command. It does not support the
{inner}, {middle}, {outer} keywords of the "run_style
command"_run_style.html.
:line
[Restrictions:]

9
doc/pair_morse.html
View File

@ -55,8 +55,8 @@ of the run time).
</P>
<HR>
<P><B>Mixing, shift, table, tail correction, per-atom energy/stress, and
restart info</B>:
<P><B>Mixing, shift, table, tail correction, per-atom energy/stress,
restart, rRESPA info</B>:
</P>
<P>None of the Morse pair styles support mixing. Thus, coefficients for
all I,J pairs must be specified explicitly.
@ -81,6 +81,11 @@ custom</A> commands.
restart files</A>, so pair_style and pair_coeff commands do
not need to be specified in an input script that reads a restart file.
</P>
<P>This pair style can only be used via the <I>pair</I> keyword of the
<A HREF = "run_style.html">run_style respa</A> command. It does not support the
<I>inner</I>, <I>middle</I>, <I>outer</I> keywords of the <A HREF = "run_style.html">run_style
command</A>.
</P>
<HR>
<P><B>Restrictions:</B>

9
doc/pair_morse.txt
View File

@ -51,8 +51,8 @@ of the run time).
:line
[Mixing, shift, table, tail correction, per-atom energy/stress, and
restart info]:
[Mixing, shift, table, tail correction, per-atom energy/stress,
restart, rRESPA info]:
None of the Morse pair styles support mixing. Thus, coefficients for
all I,J pairs must be specified explicitly.
@ -77,6 +77,11 @@ All of the Morse pair styles write their information to "binary
restart files"_restart.html, so pair_style and pair_coeff commands do
not need to be specified in an input script that reads a restart file.
This pair style can only be used via the {pair} keyword of the
"run_style respa"_run_style.html command. It does not support the
{inner}, {middle}, {outer} keywords of the "run_style
command"_run_style.html.
:line
[Restrictions:]

9
doc/pair_soft.html
View File

@ -57,8 +57,8 @@ cutoff is used.
</P>
<HR>
<P><B>Mixing, shift, table, tail correction, per-atom energy/stress, and
restart info</B>:
<P><B>Mixing, shift, table, tail correction, per-atom energy/stress,
restart, rRESPA info</B>:
</P>
<P>For atom type pairs I,J and I != J, the Astart, Astop coefficients and
cutoff distance for this pair style can be mixed. Astart and Atop are
@ -81,6 +81,11 @@ commands.
files</A>, so pair_style and pair_coeff commands do not need
to be specified in an input script that reads a restart file.
</P>
<P>This pair style can only be used via the <I>pair</I> keyword of the
<A HREF = "run_style.html">run_style respa</A> command. It does not support the
<I>inner</I>, <I>middle</I>, <I>outer</I> keywords of the <A HREF = "run_style.html">run_style
command</A>.
</P>
<HR>
<P><B>Restrictions:</B> none

9
doc/pair_soft.txt
View File

@ -54,8 +54,8 @@ cutoff is used.
:line
[Mixing, shift, table, tail correction, per-atom energy/stress, and
restart info]:
[Mixing, shift, table, tail correction, per-atom energy/stress,
restart, rRESPA info]:
For atom type pairs I,J and I != J, the Astart, Astop coefficients and
cutoff distance for this pair style can be mixed. Astart and Atop are
@ -78,6 +78,11 @@ This pair style writes its information to "binary restart
files"_restart.html, so pair_style and pair_coeff commands do not need
to be specified in an input script that reads a restart file.
This pair style can only be used via the {pair} keyword of the
"run_style respa"_run_style.html command. It does not support the
{inner}, {middle}, {outer} keywords of the "run_style
command"_run_style.html.
:line
[Restrictions:] none

9
doc/pair_sw.html
View File

@ -111,8 +111,8 @@ be set to 0.0 if desired.
</P>
<HR>
<P><B>Mixing, shift, table, tail correction, per-atom energy/stress, and
restart info</B>:
<P><B>Mixing, shift, table, tail correction, per-atom energy/stress,
restart, rRESPA info</B>:
</P>
<P>For atom type pairs I,J and I != J, where types I and J correspond to
two different element types, mixing is performed by LAMMPS as
@ -131,6 +131,11 @@ files</A>, since it is stored in potential files. Thus, you
need to re-specify the pair_style and pair_coeff commands in an input
script that reads a restart file.
</P>
<P>This pair style can only be used via the <I>pair</I> keyword of the
<A HREF = "run_style.html">run_style respa</A> command. It does not support the
<I>inner</I>, <I>middle</I>, <I>outer</I> keywords of the <A HREF = "run_style.html">run_style
command</A>.
</P>
<HR>
<P><B>Restrictions:</B>

9
doc/pair_sw.txt
View File

@ -108,8 +108,8 @@ be set to 0.0 if desired.
:line
[Mixing, shift, table, tail correction, per-atom energy/stress, and
restart info]:
[Mixing, shift, table, tail correction, per-atom energy/stress,
restart, rRESPA info]:
For atom type pairs I,J and I != J, where types I and J correspond to
two different element types, mixing is performed by LAMMPS as
@ -128,6 +128,11 @@ files"_restart.html, since it is stored in potential files. Thus, you
need to re-specify the pair_style and pair_coeff commands in an input
script that reads a restart file.
This pair style can only be used via the {pair} keyword of the
"run_style respa"_run_style.html command. It does not support the
{inner}, {middle}, {outer} keywords of the "run_style
command"_run_style.html.
:line
[Restrictions:]

9
doc/pair_table.html
View File

@ -142,8 +142,8 @@ one that matches the specified keyword.
</P>
<HR>
<P><B>Mixing, shift, table, tail correction, per-atom energy/stress, and
restart info</B>:
<P><B>Mixing, shift, table, tail correction, per-atom energy/stress,
restart, rRESPA info</B>:
</P>
<P>This pair style does not support mixing. Thus, coefficients for all
I,J pairs must be specified explicitly.
@ -163,6 +163,11 @@ However, the coefficient information is not stored in the restart
file, since it is tabulated in the potential files. Thus, pair_coeff
commands do need to be specified in the restart input script.
</P>
<P>This pair style can only be used via the <I>pair</I> keyword of the
<A HREF = "run_style.html">run_style respa</A> command. It does not support the
<I>inner</I>, <I>middle</I>, <I>outer</I> keywords of the <A HREF = "run_style.html">run_style
command</A>.
</P>
<HR>
<P><B>Restrictions:</B> none

9
doc/pair_table.txt
View File

@ -139,8 +139,8 @@ one that matches the specified keyword.
:line
[Mixing, shift, table, tail correction, per-atom energy/stress, and
restart info]:
[Mixing, shift, table, tail correction, per-atom energy/stress,
restart, rRESPA info]:
This pair style does not support mixing. Thus, coefficients for all
I,J pairs must be specified explicitly.
@ -160,6 +160,11 @@ However, the coefficient information is not stored in the restart
file, since it is tabulated in the potential files. Thus, pair_coeff
commands do need to be specified in the restart input script.
This pair style can only be used via the {pair} keyword of the
"run_style respa"_run_style.html command. It does not support the
{inner}, {middle}, {outer} keywords of the "run_style
command"_run_style.html.
:line
[Restrictions:] none

9
doc/pair_tersoff.html
View File

@ -115,8 +115,8 @@ are not used for anything and can be set to 0.0 if desired.
</P>
<HR>
<P><B>Mixing, shift, table, tail correction, per-atom energy/stress, and
restart info</B>:
<P><B>Mixing, shift, table, tail correction, per-atom energy/stress,
restart, rRESPA info</B>:
</P>
<P>For atom type pairs I,J and I != J, where types I and J correspond to
two different element types, mixing is performed by LAMMPS as
@ -135,6 +135,11 @@ files</A>, since it is stored in potential files. Thus, you
need to re-specify the pair_style and pair_coeff commands in an input
script that reads a restart file.
</P>
<P>This pair style can only be used via the <I>pair</I> keyword of the
<A HREF = "run_style.html">run_style respa</A> command. It does not support the
<I>inner</I>, <I>middle</I>, <I>outer</I> keywords of the <A HREF = "run_style.html">run_style
command</A>.
</P>
<HR>
<P><B>Restrictions:</B>

9
doc/pair_tersoff.txt
View File

@ -112,8 +112,8 @@ are not used for anything and can be set to 0.0 if desired.
:line
[Mixing, shift, table, tail correction, per-atom energy/stress, and
restart info]:
[Mixing, shift, table, tail correction, per-atom energy/stress,
restart, rRESPA info]:
For atom type pairs I,J and I != J, where types I and J correspond to
two different element types, mixing is performed by LAMMPS as
@ -132,6 +132,11 @@ files"_restart.html, since it is stored in potential files. Thus, you
need to re-specify the pair_style and pair_coeff commands in an input
script that reads a restart file.
This pair style can only be used via the {pair} keyword of the
"run_style respa"_run_style.html command. It does not support the
{inner}, {middle}, {outer} keywords of the "run_style
command"_run_style.html.
:line
[Restrictions:]

9
doc/pair_yukawa.html
View File

@ -46,8 +46,8 @@ cutoff is used.
</P>
<HR>
<P><B>Mixing, shift, table, tail correction, per-atom energy/stress, and
restart info</B>:
<P><B>Mixing, shift, table, tail correction, per-atom energy/stress,
restart, rRESPA info</B>:
</P>
<P>For atom type pairs I,J and I != J, the A coefficient and cutoff
distance for this pair style can be mixed. A is an energy value mixed
@ -73,6 +73,11 @@ commands.
files</A>, so pair_style and pair_coeff commands do not need
to be specified in an input script that reads a restart file.
</P>
<P>This pair style can only be used via the <I>pair</I> keyword of the
<A HREF = "run_style.html">run_style respa</A> command. It does not support the
<I>inner</I>, <I>middle</I>, <I>outer</I> keywords of the <A HREF = "run_style.html">run_style
command</A>.
</P>
<HR>
<P><B>Restrictions:</B> none

9
doc/pair_yukawa.txt
View File

@ -43,8 +43,8 @@ cutoff is used.
:line
[Mixing, shift, table, tail correction, per-atom energy/stress, and
restart info]:
[Mixing, shift, table, tail correction, per-atom energy/stress,
restart, rRESPA info]:
For atom type pairs I,J and I != J, the A coefficient and cutoff
distance for this pair style can be mixed. A is an energy value mixed
@ -70,6 +70,11 @@ This pair style writes its information to "binary restart
files"_restart.html, so pair_style and pair_coeff commands do not need
to be specified in an input script that reads a restart file.
This pair style can only be used via the {pair} keyword of the
"run_style respa"_run_style.html command. It does not support the
{inner}, {middle}, {outer} keywords of the "run_style
command"_run_style.html.
:line
[Restrictions:] none

20
doc/run_style.html
View File

@ -91,13 +91,19 @@ outermost level, and kspace forces are computed where pair forces are.
The inner, middle, outer forces have no defaults.
</P>
<P>The <I>inner</I> and <I>middle</I> keywords take additional arguments for
cutoffs that are used by the force computations. If the 2 cutoffs for
<I>inner</I> are 5.0 and 6.0, this means that all pairs up to 6.0 apart are
computed by the inner force. Those between 5.0 and 6.0 have their
force go ramped to 0.0 so the overlap with the next regime (middle or
outer) is smooth. The next regime (middle or outer) will compute
forces for all pairs from 5.0 outward, with those from 5.0 to 6.0
having their value ramped in an inverse manner.
cutoffs that are used by the pairwise force computations. If the 2
cutoffs for <I>inner</I> are 5.0 and 6.0, this means that all pairs up to
6.0 apart are computed by the inner force. Those between 5.0 and 6.0
have their force go ramped to 0.0 so the overlap with the next regime
(middle or outer) is smooth. The next regime (middle or outer) will
compute forces for all pairs from 5.0 outward, with those from 5.0 to
6.0 having their value ramped in an inverse manner.
</P>
<P>Only some pair potentials support the use of the <I>inner</I> and <I>middle</I>
and <I>outer</I> keywords. If not, only the <I>pair</I> keyword can be used
with that pair style, meaning all pairwise forces are computed at the
same rRESPA level. See the doc pages for individual pair styles for
details.
</P>
<P>When using rRESPA (or for any MD simulation) care must be taken to
choose a timestep size(s) that insures the Hamiltonian for the chosen

20
doc/run_style.txt
View File

@ -86,13 +86,19 @@ outermost level, and kspace forces are computed where pair forces are.
The inner, middle, outer forces have no defaults.
The {inner} and {middle} keywords take additional arguments for
cutoffs that are used by the force computations. If the 2 cutoffs for
{inner} are 5.0 and 6.0, this means that all pairs up to 6.0 apart are
computed by the inner force. Those between 5.0 and 6.0 have their
force go ramped to 0.0 so the overlap with the next regime (middle or
outer) is smooth. The next regime (middle or outer) will compute
forces for all pairs from 5.0 outward, with those from 5.0 to 6.0
having their value ramped in an inverse manner.
cutoffs that are used by the pairwise force computations. If the 2
cutoffs for {inner} are 5.0 and 6.0, this means that all pairs up to
6.0 apart are computed by the inner force. Those between 5.0 and 6.0
have their force go ramped to 0.0 so the overlap with the next regime
(middle or outer) is smooth. The next regime (middle or outer) will
compute forces for all pairs from 5.0 outward, with those from 5.0 to
6.0 having their value ramped in an inverse manner.
Only some pair potentials support the use of the {inner} and {middle}
and {outer} keywords. If not, only the {pair} keyword can be used
with that pair style, meaning all pairwise forces are computed at the
same rRESPA level. See the doc pages for individual pair styles for
details.
When using rRESPA (or for any MD simulation) care must be taken to
choose a timestep size(s) that insures the Hamiltonian for the chosen