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7
doc/Section_accelerate.html
View File

@ -106,6 +106,13 @@ to 20% savings.
<H4><A NAME = "10_2"></A>10.2 GPU package
</H4>
<P>Additional requirements in your input script to run the styles with a
<I>gpu</I> suffix are as follows:
</P>
<P>The <A HREF = "newton.html">newton pair</A> setting must be <I>off</I> and the <A HREF = "fix_gpu.html">fix
gpu</A> command must be used. The fix controls the GPU
selection and initialization steps.
</P>
<P>The GPU package was developed by Mike Brown at ORNL.
</P>
<P>A few LAMMPS <A HREF = "pair_style.html">pair styles</A> can be run on graphical

9
doc/Section_accelerate.txt
View File

@ -102,6 +102,15 @@ to 20% savings.
10.2 GPU package :h4,link(10_2)
Additional requirements in your input script to run the styles with a
{gpu} suffix are as follows:
The "newton pair"_newton.html setting must be {off} and the "fix
gpu"_fix_gpu.html command must be used. The fix controls the GPU
selection and initialization steps.
The GPU package was developed by Mike Brown at ORNL.
A few LAMMPS "pair styles"_pair_style.html can be run on graphical

43
doc/kspace_style.html
View File

@ -76,9 +76,6 @@ long-range potentials.
<P>Currently, only the <I>ewald/n</I> style can be used with non-orthogonal
(triclinic symmetry) simulation boxes.
</P>
<P>The <I>pppm/gpu/single</I> and <I>pppm/gpu/double</I> styles are GPU-enabled
version of <I>pppm</I>. See more details below.
</P>
<HR>
<P>When a kspace style is used, a pair style that includes the
@ -99,23 +96,30 @@ options of the K-space solvers that can be set.
</P>
<HR>
<P>The <I>pppm/gpu/single</I> style performs single precision charge
assignment and force interpolation calculations on the GPU. The
<I>pppm/gpu/double</I> style performs the mesh calculations on the GPU in
double precision. In both cases, FFT solves are calculated on the CPU.
If either <I>pppm/gpu/single</I> or <I>pppm/gpu/double</I> are used with a
GPU-enabled pair style, part of the PPPM calculation can be performed
concurrently on the GPU while other calculations for non-bonded and
bonded force calculation are performed on the CPU.
<P>Styles with a <I>cuda</I>, <I>gpu/single</I>, <I>gpu/double</I>, or <I>opt</I> suffix are
functionally the same as the corresponding style without the suffix.
They have been optimized to run faster, depending on your available
hardware, as discussed in <A HREF = "Section_accelerate.html">this section</A> of
the manual. The accelerated styles take the same arguments and should
produce the same results, except for round-off and precision issues.
</P>
<P>See <A HREF = "doc/Section_accerate.html">this section</A> of the manual for more
details.
<P>More specifically, the <I>pppm/gpu/single</I> style performs single
precision charge assignment and force interpolation calculations on
the GPU. The <I>pppm/gpu/double</I> style performs the mesh calculations
on the GPU in double precision. In both cases, FFT solves are
calculated on the CPU. If either <I>pppm/gpu/single</I> or
<I>pppm/gpu/double</I> are used with a GPU-enabled pair style, part of the
PPPM calculation can be performed concurrently on the GPU while other
calculations for non-bonded and bonded force calculation are performed
on the CPU.
</P>
<P>Additional requirements in your input script to run with GPU-enabled
PPPM styles are as follows:
<P>These accelerated styles are part of the "user-cuda", "gpu", and "opt"
packages respectively. They are only enabled if LAMMPS was built with
those packages. See the <A HREF = "Section_start.html#2_3">Making LAMMPS</A>
section for more info.
</P>
<P>The <A HREF = "fix_gpu.html">fix gpu</A> command must be used. The fix controls the
GPU selection and initialization steps.
<P>See <A HREF = "Section_accelerate.html">this section</A> of the manual for more
instructions on how to use the accelerated styles effectively.
</P>
<P><B>Restrictions:</B>
</P>
@ -132,11 +136,6 @@ LAMMPS</A> section for more info.
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>The <I>pppm/gpu/single</I> and <I>pppm/gpu/double</I> styles are part of the
"gpu" package. They are 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>

43
doc/kspace_style.txt
View File

@ -71,9 +71,6 @@ long-range potentials.
Currently, only the {ewald/n} style can be used with non-orthogonal
(triclinic symmetry) simulation boxes.
The {pppm/gpu/single} and {pppm/gpu/double} styles are GPU-enabled
version of {pppm}. See more details below.
:line
When a kspace style is used, a pair style that includes the
@ -94,23 +91,30 @@ options of the K-space solvers that can be set.
:line
The {pppm/gpu/single} style performs single precision charge
assignment and force interpolation calculations on the GPU. The
{pppm/gpu/double} style performs the mesh calculations on the GPU in
double precision. In both cases, FFT solves are calculated on the CPU.
If either {pppm/gpu/single} or {pppm/gpu/double} are used with a
GPU-enabled pair style, part of the PPPM calculation can be performed
concurrently on the GPU while other calculations for non-bonded and
bonded force calculation are performed on the CPU.
Styles with a {cuda}, {gpu/single}, {gpu/double}, or {opt} suffix are
functionally the same as the corresponding style without the suffix.
They have been optimized to run faster, depending on your available
hardware, as discussed in "this section"_Section_accelerate.html of
the manual. The accelerated styles take the same arguments and should
produce the same results, except for round-off and precision issues.
See "this section"_doc/Section_accerate.html of the manual for more
details.
More specifically, the {pppm/gpu/single} style performs single
precision charge assignment and force interpolation calculations on
the GPU. The {pppm/gpu/double} style performs the mesh calculations
on the GPU in double precision. In both cases, FFT solves are
calculated on the CPU. If either {pppm/gpu/single} or
{pppm/gpu/double} are used with a GPU-enabled pair style, part of the
PPPM calculation can be performed concurrently on the GPU while other
calculations for non-bonded and bonded force calculation are performed
on the CPU.
Additional requirements in your input script to run with GPU-enabled
PPPM styles are as follows:
These accelerated styles are part of the "user-cuda", "gpu", and "opt"
packages respectively. They are only enabled if LAMMPS was built with
those packages. See the "Making LAMMPS"_Section_start.html#2_3
section for more info.
The "fix gpu"_fix_gpu.html command must be used. The fix controls the
GPU selection and initialization steps.
See "this section"_Section_accelerate.html of the manual for more
instructions on how to use the accelerated styles effectively.
[Restrictions:]
@ -127,11 +131,6 @@ The {ewald/n} style is part of the "user-ewaldn" package. It is only
enabled if LAMMPS was built with that package. See the "Making
LAMMPS"_Section_start.html#2_3 section for more info.
The {pppm/gpu/single} and {pppm/gpu/double} styles are part of the
"gpu" package. They are only enabled if LAMMPS was built with that
package. See the "Making LAMMPS"_Section_start.html#2_3 section for
more info.
When using a long-range pairwise TIP4P potential, you must use kspace
style {pppm/tip4p} and vice versa.

55
doc/pair_charmm.html
View File

@ -23,7 +23,7 @@
</P>
<PRE>pair_style style args
</PRE>
<UL><LI>style = <I>lj/charmm/coul/charmm</I> or <I>lj/charmm/coul/charmm/implicit</I> or <I>lj/charmm/coul/long</I> or <I>lj/charmm/coul/long/gpu</I> or <I>lj/charmm/coul/long/opt</I>
<UL><LI>style = <I>lj/charmm/coul/charmm</I> or <I>lj/charmm/coul/charmm/implicit</I> or <I>lj/charmm/coul/long</I>
<LI>args = list of arguments for a particular style
</UL>
<PRE> <I>lj/charmm/coul/charmm</I> args = inner outer (inner2) (outer2)
@ -33,9 +33,6 @@
inner, outer = global switching cutoffs for LJ (and Coulombic if only 2 args)
inner2, outer2 = global switching cutoffs for Coulombic (optional)
<I>lj/charmm/coul/long</I> args = inner outer (cutoff)
inner, outer = global switching cutoffs for LJ (and Coulombic if only 2 args)
cutoff = global cutoff for Coulombic (optional, outer is Coulombic cutoff if only 2 args)
<I>lj/charmm/coul/long/gpu</I> args = inner outer (cutoff)
inner, outer = global switching cutoffs for LJ (and Coulombic if only 2 args)
cutoff = global cutoff for Coulombic (optional, outer is Coulombic cutoff if only 2 args)
</PRE>
@ -52,8 +49,6 @@ pair_coeff * * 100.0 2.0
pair_coeff 1 1 100.0 2.0 150.0 3.5
</PRE>
<PRE>pair_style lj/charmm/coul/long 8.0 10.0
pair_style lj/charmm/coul/long/gpu 8.0 10.0
pair_style lj/charmm/coul/long/opt 8.0 10.0
pair_style lj/charmm/coul/long 8.0 10.0 9.0
pair_coeff * * 100.0 2.0
pair_coeff 1 1 100.0 2.0 150.0 3.5
@ -92,12 +87,6 @@ applied to the Coulombic term, as in the discussion for pair style
command, then the outer LJ cutoff is used as the single Coulombic
cutoff.
</P>
<P>Style <I>lj/charmm/coul/long/gpu</I> is a GPU-enabled version of style
<I>lj/charmm/coul/long</I>. See more details below.
</P>
<P>Style <I>lj/charmm/coul/long/opt</I> is an optimized version of style
<I>lj/charmm/coul/long</I>. See more details below.
</P>
<P>The following coefficients must be defined for each pair of atoms
types via the <A HREF = "pair_coeff.html">pair_coeff</A> command as in the examples
above, or in the data file or restart files read by the
@ -122,23 +111,25 @@ the pair_style command.
</P>
<HR>
<P>The styles with an <I>opt</I> suffix are identical to the corresponding
styles without the suffix, except that it is written in an optimized
fashion for faster CPU execution. See <A HREF = "doc/Section_accerate.html">this
section</A> of the manual for more details.
<P>Styles with a <I>cuda</I>, <I>gpu</I>, or <I>opt</I> suffix are functionally the same
as the corresponding style without the suffix. They have been
optimized to run faster, depending on your available hardware, as
discussed in <A HREF = "Section_accelerate.html">this section</A> of the manual.
The accelerated styles take the same arguments and should produce the
same results, except for round-off and precision issues.
</P>
<P>The styles with a <I>gpu</I> suffix are identical to the corresponding
styles without the suffix, except that each processor off-loads its
pairwise calculations to a GPU. Depending on the hardware available
on your system this can provide a speed-up. See <A HREF = "doc/Section_accerate.html">this
section</A> of the manual for more details.
<P>These accelerated styles are part of the "user-cuda", "gpu", and "opt"
packages respectively. They are only enabled if LAMMPS was built with
those packages. See the <A HREF = "Section_start.html#2_3">Making LAMMPS</A>
section for more info.
</P>
<P>Additional requirements in your input script to run the styles with a
<I>gpu</I> suffix are as follows:
<P>You can specify the accelerated styles explicitly in your input script
by including their suffix, or you can use the <A HREF = "Section_start.html#2_6">-suffix command-line
switch</A> when you invoke LAMMPS, or you can use
the <A HREF = "suffix.html">suffix</A> command in your input script.
</P>
<P>The <A HREF = "newton.html">newton pair</A> setting must be <I>off</I> and the <A HREF = "fix_gpu.html">fix
gpu</A> command must be used. The fix controls the GPU
selection and initialization steps.
<P>See <A HREF = "Section_accelerate.html">this section</A> of the manual for more
instructions on how to use the accelerated styles effectively.
</P>
<HR>
@ -154,10 +145,9 @@ command for details.
<A HREF = "pair_modify.html">pair_modify</A> shift option, since the Lennard-Jones
portion of the pair interaction is smoothed to 0.0 at the cutoff.
</P>
<P>The <I>lj/charmm/coul/long</I> and <I>lj/charmm/coul/long/opt</I> pair styles
support the <A HREF = "pair_modify.html">pair_modify</A> table option since they can
tabulate the short-range portion of the long-range Coulombic
interaction.
<P>The <I>lj/charmm/coul/long</I> style supports the
<A HREF = "pair_modify.html">pair_modify</A> table option since it can tabulate the
short-range portion of the long-range Coulombic interaction.
</P>
<P>None of the lj/charmm pair styles support the
<A HREF = "pair_modify.html">pair_modify</A> tail option for adding long-range tail
@ -181,9 +171,8 @@ support the <I>pair</I> keyword of run_style respa. See the
</P>
<P>The <I>lj/charmm/coul/charmm</I> and <I>lj/charmm/coul/charmm/implicit</I>
styles are part of the "molecule" package. The <I>lj/charmm/coul/long</I>
style is part of the "kspace" package. The styles with an <I>opt</I> or
<I>gpu</I> suffix are part of the "opt" or "gpu" packages. They are only
enabled if LAMMPS was built with those packages. See the <A HREF = "Section_start.html#2_3">Making
style is part of the "kspace" package. They are only enabled if
LAMMPS was built with those packages. See the <A HREF = "Section_start.html#2_3">Making
LAMMPS</A> section for more info. Note that the
molecule and kspace packages are installed by default.
</P>

55
doc/pair_charmm.txt
View File

@ -16,7 +16,7 @@ pair_style lj/charmm/coul/long/opt command :h3
pair_style style args :pre
style = {lj/charmm/coul/charmm} or {lj/charmm/coul/charmm/implicit} or {lj/charmm/coul/long} or {lj/charmm/coul/long/gpu} or {lj/charmm/coul/long/opt}
style = {lj/charmm/coul/charmm} or {lj/charmm/coul/charmm/implicit} or {lj/charmm/coul/long}
args = list of arguments for a particular style :ul
{lj/charmm/coul/charmm} args = inner outer (inner2) (outer2)
inner, outer = global switching cutoffs for Lennard Jones (and Coulombic if only 2 args)
@ -25,9 +25,6 @@ args = list of arguments for a particular style :ul
inner, outer = global switching cutoffs for LJ (and Coulombic if only 2 args)
inner2, outer2 = global switching cutoffs for Coulombic (optional)
{lj/charmm/coul/long} args = inner outer (cutoff)
inner, outer = global switching cutoffs for LJ (and Coulombic if only 2 args)
cutoff = global cutoff for Coulombic (optional, outer is Coulombic cutoff if only 2 args)
{lj/charmm/coul/long/gpu} args = inner outer (cutoff)
inner, outer = global switching cutoffs for LJ (and Coulombic if only 2 args)
cutoff = global cutoff for Coulombic (optional, outer is Coulombic cutoff if only 2 args) :pre
@ -44,8 +41,6 @@ pair_coeff * * 100.0 2.0
pair_coeff 1 1 100.0 2.0 150.0 3.5 :pre
pair_style lj/charmm/coul/long 8.0 10.0
pair_style lj/charmm/coul/long/gpu 8.0 10.0
pair_style lj/charmm/coul/long/opt 8.0 10.0
pair_style lj/charmm/coul/long 8.0 10.0 9.0
pair_coeff * * 100.0 2.0
pair_coeff 1 1 100.0 2.0 150.0 3.5 :pre
@ -84,12 +79,6 @@ applied to the Coulombic term, as in the discussion for pair style
command, then the outer LJ cutoff is used as the single Coulombic
cutoff.
Style {lj/charmm/coul/long/gpu} is a GPU-enabled version of style
{lj/charmm/coul/long}. See more details below.
Style {lj/charmm/coul/long/opt} is an optimized version of style
{lj/charmm/coul/long}. See more details below.
The following coefficients must be defined for each pair of atoms
types via the "pair_coeff"_pair_coeff.html command as in the examples
above, or in the data file or restart files read by the
@ -114,23 +103,25 @@ the pair_style command.
:line
The styles with an {opt} suffix are identical to the corresponding
styles without the suffix, except that it is written in an optimized
fashion for faster CPU execution. See "this
section"_doc/Section_accerate.html of the manual for more details.
Styles with a {cuda}, {gpu}, or {opt} suffix are functionally the same
as the corresponding style without the suffix. They have been
optimized to run faster, depending on your available hardware, as
discussed in "this section"_Section_accelerate.html of the manual.
The accelerated styles take the same arguments and should produce the
same results, except for round-off and precision issues.
The styles with a {gpu} suffix are identical to the corresponding
styles without the suffix, except that each processor off-loads its
pairwise calculations to a GPU. Depending on the hardware available
on your system this can provide a speed-up. See "this
section"_doc/Section_accerate.html of the manual for more details.
These accelerated styles are part of the "user-cuda", "gpu", and "opt"
packages respectively. They are only enabled if LAMMPS was built with
those packages. See the "Making LAMMPS"_Section_start.html#2_3
section for more info.
Additional requirements in your input script to run the styles with a
{gpu} suffix are as follows:
You can specify the accelerated styles explicitly in your input script
by including their suffix, or you can use the "-suffix command-line
switch"_Section_start.html#2_6 when you invoke LAMMPS, or you can use
the "suffix"_suffix.html command in your input script.
The "newton pair"_newton.html setting must be {off} and the "fix
gpu"_fix_gpu.html command must be used. The fix controls the GPU
selection and initialization steps.
See "this section"_Section_accelerate.html of the manual for more
instructions on how to use the accelerated styles effectively.
:line
@ -146,10 +137,9 @@ None of the lj/charmm pair styles support the
"pair_modify"_pair_modify.html shift option, since the Lennard-Jones
portion of the pair interaction is smoothed to 0.0 at the cutoff.
The {lj/charmm/coul/long} and {lj/charmm/coul/long/opt} pair styles
support the "pair_modify"_pair_modify.html table option since they can
tabulate the short-range portion of the long-range Coulombic
interaction.
The {lj/charmm/coul/long} style supports the
"pair_modify"_pair_modify.html table option since it can tabulate the
short-range portion of the long-range Coulombic interaction.
None of the lj/charmm pair styles support the
"pair_modify"_pair_modify.html tail option for adding long-range tail
@ -173,9 +163,8 @@ support the {pair} keyword of run_style respa. See the
The {lj/charmm/coul/charmm} and {lj/charmm/coul/charmm/implicit}
styles are part of the "molecule" package. The {lj/charmm/coul/long}
style is part of the "kspace" package. The styles with an {opt} or
{gpu} suffix are part of the "opt" or "gpu" packages. They are only
enabled if LAMMPS was built with those packages. See the "Making
style is part of the "kspace" package. They are only enabled if
LAMMPS was built with those packages. See the "Making
LAMMPS"_Section_start.html#2_3 section for more info. Note that the
molecule and kspace packages are installed by default.

45
doc/pair_class2.html
View File

@ -23,7 +23,7 @@
</P>
<PRE>pair_style style args
</PRE>
<UL><LI>style = <I>lj/class2</I> or <I>lj/class2/gpu</I> or <I>lj/class2/coul/cut</I> or <I>lj/class2/coul/long</I> or <I>lj/class2/coul/long/gpu</I>
<UL><LI>style = <I>lj/class2</I> or <I>lj/class2/coul/cut</I> or <I>lj/class2/coul/long</I>
<LI>args = list of arguments for a particular style
</UL>
<PRE> <I>lj/class2</I> args = cutoff
@ -38,7 +38,6 @@
<P><B>Examples:</B>
</P>
<PRE>pair_style lj/class2 10.0
pair_style lj/class2/gpu 10.0
pair_coeff * * 100.0 2.5
pair_coeff 1 2* 100.0 2.5 9.0
</PRE>
@ -49,7 +48,6 @@ pair_coeff 1 1 100.0 3.5 9.0
pair_coeff 1 1 100.0 3.5 9.0 9.0
</PRE>
<PRE>pair_style lj/class2/coul/long 10.0
pair_style lj/class2/coul/long/gpu 10.0
pair_style lj/class2/coul/long 10.0 8.0
pair_coeff * * 100.0 3.0
pair_coeff 1 1 100.0 3.5 9.0
@ -62,16 +60,10 @@ pair_coeff 1 1 100.0 3.5 9.0
</CENTER>
<P>Rc is the cutoff.
</P>
<P>Style <I>lj/class2/gpu</I> is a GPU-enabled version of style <I>lj/class2</I>.
See more details below.
</P>
<P>The <I>lj/class2/coul/cut</I> and <I>lj/class2/coul/long</I> styles add a
Coulombic term as described for the <A HREF = "pair_lj.html">lj/cut</A> pair
styles.
</P>
<P>Style <I>lj/class2/coul/long/gpu</I> is a GPU-enabled version of style
<I>lj/class2/coul/long</I>. See more details below.
</P>
<P>See <A HREF = "#Sun">(Sun)</A> for a description of the COMPASS class2 force field.
</P>
<P>The following coefficients must be defined for each pair of atoms
@ -110,18 +102,25 @@ cutoff distance.
</P>
<HR>
<P>The styles with a <I>gpu</I> suffix are identical to the corresponding
styles without the suffix, except that each processor off-loads its
pairwise calculations to a GPU. Depending on the hardware available
on your system this can provide a speed-up. See <A HREF = "doc/Section_accerate.html">this
section</A> of the manual for more details.
<P>Styles with a <I>cuda</I>, <I>gpu</I>, or <I>opt</I> suffix are functionally the same
as the corresponding style without the suffix. They have been
optimized to run faster, depending on your available hardware, as
discussed in <A HREF = "Section_accelerate.html">this section</A> of the manual.
The accelerated styles take the same arguments and should produce the
same results, except for round-off and precision issues.
</P>
<P>Additional requirements in your input script to run the styles with a
<I>gpu</I> suffix are as follows:
<P>These accelerated styles are part of the "user-cuda", "gpu", and "opt"
packages respectively. They are only enabled if LAMMPS was built with
those packages. See the <A HREF = "Section_start.html#2_3">Making LAMMPS</A>
section for more info.
</P>
<P>The <A HREF = "newton.html">newton pair</A> setting must be <I>off</I> and the <A HREF = "fix_gpu.html">fix
gpu</A> command must be used. The fix controls the GPU
selection and initialization steps.
<P>You can specify the accelerated styles explicitly in your input script
by including their suffix, or you can use the <A HREF = "Section_start.html#2_6">-suffix command-line
switch</A> when you invoke LAMMPS, or you can use
the <A HREF = "suffix.html">suffix</A> command in your input script.
</P>
<P>See <A HREF = "Section_accelerate.html">this section</A> of the manual for more
instructions on how to use the accelerated styles effectively.
</P>
<P><B>Mixing, shift, table, tail correction, restart, rRESPA info</B>:
</P>
@ -155,11 +154,9 @@ support the <I>inner</I>, <I>middle</I>, <I>outer</I> keywords.
</P>
<P><B>Restrictions:</B>
</P>
<P>All of these pair styles, except those ending in "gpu", are part of
the "class2" package. They are only enabled if LAMMPS was built with
that package. The styles with a <I>gpu</I> suffix are part of the "gpu"
package. They are 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>These styles are part of the "class2" package. They are 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><B>Related commands:</B>
</P>

45
doc/pair_class2.txt
View File

@ -16,7 +16,7 @@ pair_style lj/class2/coul/long/gpu command :h3
pair_style style args :pre
style = {lj/class2} or {lj/class2/gpu} or {lj/class2/coul/cut} or {lj/class2/coul/long} or {lj/class2/coul/long/gpu}
style = {lj/class2} or {lj/class2/coul/cut} or {lj/class2/coul/long}
args = list of arguments for a particular style :ul
{lj/class2} args = cutoff
cutoff = global cutoff for class 2 interactions (distance units)
@ -30,7 +30,6 @@ args = list of arguments for a particular style :ul
[Examples:]
pair_style lj/class2 10.0
pair_style lj/class2/gpu 10.0
pair_coeff * * 100.0 2.5
pair_coeff 1 2* 100.0 2.5 9.0 :pre
@ -41,7 +40,6 @@ pair_coeff 1 1 100.0 3.5 9.0
pair_coeff 1 1 100.0 3.5 9.0 9.0 :pre
pair_style lj/class2/coul/long 10.0
pair_style lj/class2/coul/long/gpu 10.0
pair_style lj/class2/coul/long 10.0 8.0
pair_coeff * * 100.0 3.0
pair_coeff 1 1 100.0 3.5 9.0 :pre
@ -54,16 +52,10 @@ The {lj/class2} styles compute a 6/9 Lennard-Jones potential given by
Rc is the cutoff.
Style {lj/class2/gpu} is a GPU-enabled version of style {lj/class2}.
See more details below.
The {lj/class2/coul/cut} and {lj/class2/coul/long} styles add a
Coulombic term as described for the "lj/cut"_pair_lj.html pair
styles.
Style {lj/class2/coul/long/gpu} is a GPU-enabled version of style
{lj/class2/coul/long}. See more details below.
See "(Sun)"_#Sun for a description of the COMPASS class2 force field.
The following coefficients must be defined for each pair of atoms
@ -102,18 +94,25 @@ cutoff distance.
:line
The styles with a {gpu} suffix are identical to the corresponding
styles without the suffix, except that each processor off-loads its
pairwise calculations to a GPU. Depending on the hardware available
on your system this can provide a speed-up. See "this
section"_doc/Section_accerate.html of the manual for more details.
Styles with a {cuda}, {gpu}, or {opt} suffix are functionally the same
as the corresponding style without the suffix. They have been
optimized to run faster, depending on your available hardware, as
discussed in "this section"_Section_accelerate.html of the manual.
The accelerated styles take the same arguments and should produce the
same results, except for round-off and precision issues.
Additional requirements in your input script to run the styles with a
{gpu} suffix are as follows:
These accelerated styles are part of the "user-cuda", "gpu", and "opt"
packages respectively. They are only enabled if LAMMPS was built with
those packages. See the "Making LAMMPS"_Section_start.html#2_3
section for more info.
The "newton pair"_newton.html setting must be {off} and the "fix
gpu"_fix_gpu.html command must be used. The fix controls the GPU
selection and initialization steps.
You can specify the accelerated styles explicitly in your input script
by including their suffix, or you can use the "-suffix command-line
switch"_Section_start.html#2_6 when you invoke LAMMPS, or you can use
the "suffix"_suffix.html command in your input script.
See "this section"_Section_accelerate.html of the manual for more
instructions on how to use the accelerated styles effectively.
[Mixing, shift, table, tail correction, restart, rRESPA info]:
@ -147,11 +146,9 @@ support the {inner}, {middle}, {outer} keywords.
[Restrictions:]
All of these pair styles, except those ending in "gpu", are part of
the "class2" package. They are only enabled if LAMMPS was built with
that package. The styles with a {gpu} suffix are part of the "gpu"
package. They are only enabled if LAMMPS was built with that package.
See the "Making LAMMPS"_Section_start.html#2_3 section for more info.
These styles are part of the "class2" package. They are only enabled
if LAMMPS was built with that package. See the "Making
LAMMPS"_Section_start.html#2_3 section for more info.
[Related commands:]

49
doc/pair_cmm.html
View File

@ -23,13 +23,11 @@
</P>
<PRE>pair_style style args
</PRE>
<UL><LI>style = <I>cg/cmm</I> or <I>cg/cmm/gpu</I> or <I>cg/cmm/coul/cut</I> or <I>cg/cmm/coul/long</I> or <I>cg/cmm/coul/long/gpu</I>
<UL><LI>style = <I>cg/cmm</I> or <I>cg/cmm/coul/cut</I> or <I>cg/cmm/coul/long</I>
<LI>args = list of arguments for a particular style
</UL>
<PRE> <I>cg/cmm</I> args = cutoff
cutoff = global cutoff for Lennard Jones interactions (distance units)
<I>cg/cmm/gpu</I> args = cutoff
cutoff = global cutoff for Lennard Jones interactions (distance units)
<I>cg/cmm/coul/cut</I> args = cutoff (cutoff2) (kappa)
cutoff = global cutoff for LJ (and Coulombic if only 1 arg) (distance units)
cutoff2 = global cutoff for Coulombic (optional) (distance units)
@ -38,10 +36,6 @@
cutoff = global cutoff for LJ (and Coulombic if only 1 arg) (distance units)
cutoff2 = global cutoff for Coulombic (optional) (distance units)
</PRE>
<PRE> <I>cg/cmm/coul/long/gpu</I> args = cutoff (cutoff2)
cutoff = global cutoff for LJ (and Coulombic if only 1 arg) (distance units)
cutoff2 = global cutoff for Coulombic (optional) (distance units)
</PRE>
<P><B>Examples:</B>
</P>
<PRE>pair_style cg/cmm 2.5
@ -65,9 +59,6 @@ given by
<P>as required for the CMM Coarse-grained MD parametrization discussed in
<A HREF = "#Shinoda">(Shinoda)</A> and <A HREF = "#DeVane">(DeVane)</A>. Rc is the cutoff.
</P>
<P>Style <I>cg/cmm/gpu</I> is a GPU-enabled version of style <I>cg/cmm</I>. See
more details below.
</P>
<P>Style <I>cg/cmm/coul/cut</I> adds a Coulombic pairwise interaction given by
</P>
<CENTER><IMG SRC = "Eqs/pair_coulomb.jpg">
@ -96,9 +87,6 @@ option. The Coulombic cutoff specified for this style means that
pairwise interactions within this distance are computed directly;
interactions outside that distance are computed in reciprocal space.
</P>
<P>Style <I>cg/cmm/coul/long/gpu</I> is a GPU-enabled version of style
<I>cg/cmm/coul/long</I>. See more details below.
</P>
<P>The following coefficients must be defined for each pair of atoms
types via the <A HREF = "pair_coeff.html">pair_coeff</A> command as in the examples
above, or in the data file or restart files read by the
@ -129,18 +117,25 @@ pair_style command.
</P>
<HR>
<P>The styles with a <I>gpu</I> suffix are identical to the corresponding
styles without the suffix, except that each processor off-loads its
pairwise calculations to a GPU. Depending on the hardware available
on your system this can provide a speed-up. See <A HREF = "doc/Section_accerate.html">this
section</A> of the manual for more details.
<P>Styles with a <I>cuda</I>, <I>gpu</I>, or <I>opt</I> suffix are functionally the same
as the corresponding style without the suffix. They have been
optimized to run faster, depending on your available hardware, as
discussed in <A HREF = "Section_accelerate.html">this section</A> of the manual.
The accelerated styles take the same arguments and should produce the
same results, except for round-off and precision issues.
</P>
<P>Additional requirements in your input script to run the styles with a
<I>gpu</I> suffix are as follows:
<P>These accelerated styles are part of the "user-cuda", "gpu", and "opt"
packages respectively. They are only enabled if LAMMPS was built with
those packages. See the <A HREF = "Section_start.html#2_3">Making LAMMPS</A>
section for more info.
</P>
<P>The <A HREF = "newton.html">newton pair</A> setting must be <I>off</I> and the <A HREF = "fix_gpu.html">fix
gpu</A> command must be used. The fix controls the GPU
selection and initialization steps.
<P>You can specify the accelerated styles explicitly in your input script
by including their suffix, or you can use the <A HREF = "Section_start.html#2_6">-suffix command-line
switch</A> when you invoke LAMMPS, or you can use
the <A HREF = "suffix.html">suffix</A> command in your input script.
</P>
<P>See <A HREF = "Section_accelerate.html">this section</A> of the manual for more
instructions on how to use the accelerated styles effectively.
</P>
<HR>
@ -175,12 +170,10 @@ See the <A HREF = "run_style.html">run_style</A> command for details.
<P><B>Restrictions:</B>
</P>
<P>All of the cg/cmm pair styles are part of the "user-cg-cmm"
package. They are only enabled if LAMMPS was built with that package.
<P>All of the cg/cmm pair styles are part of the "user-cg-cmm" package.
The <I>cg/cmm/coul/long</I> style also requires the "kspace" package to be
built (which is enabled by default). The styles with a <I>gpu</I> suffix
are part of the "gpu" package. They are only enabled if LAMMPS was
built with that package. See the <A HREF = "Section_start.html#2_3">Making
built (which is enabled by default). They are 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><B>Related commands:</B>

48
doc/pair_cmm.txt
View File

@ -16,12 +16,10 @@ pair_style cg/cmm/coul/long/gpu command :h3
pair_style style args :pre
style = {cg/cmm} or {cg/cmm/gpu} or {cg/cmm/coul/cut} or {cg/cmm/coul/long} or {cg/cmm/coul/long/gpu}
style = {cg/cmm} or {cg/cmm/coul/cut} or {cg/cmm/coul/long}
args = list of arguments for a particular style :ul
{cg/cmm} args = cutoff
cutoff = global cutoff for Lennard Jones interactions (distance units)
{cg/cmm/gpu} args = cutoff
cutoff = global cutoff for Lennard Jones interactions (distance units)
{cg/cmm/coul/cut} args = cutoff (cutoff2) (kappa)
cutoff = global cutoff for LJ (and Coulombic if only 1 arg) (distance units)
cutoff2 = global cutoff for Coulombic (optional) (distance units)
@ -29,9 +27,6 @@ args = list of arguments for a particular style :ul
{cg/cmm/coul/long} args = cutoff (cutoff2)
cutoff = global cutoff for LJ (and Coulombic if only 1 arg) (distance units)
cutoff2 = global cutoff for Coulombic (optional) (distance units) :pre
{cg/cmm/coul/long/gpu} args = cutoff (cutoff2)
cutoff = global cutoff for LJ (and Coulombic if only 1 arg) (distance units)
cutoff2 = global cutoff for Coulombic (optional) (distance units) :pre
[Examples:]
@ -56,9 +51,6 @@ given by
as required for the CMM Coarse-grained MD parametrization discussed in
"(Shinoda)"_#Shinoda and "(DeVane)"_#DeVane. Rc is the cutoff.
Style {cg/cmm/gpu} is a GPU-enabled version of style {cg/cmm}. See
more details below.
Style {cg/cmm/coul/cut} adds a Coulombic pairwise interaction given by
:c,image(Eqs/pair_coulomb.jpg)
@ -87,9 +79,6 @@ option. The Coulombic cutoff specified for this style means that
pairwise interactions within this distance are computed directly;
interactions outside that distance are computed in reciprocal space.
Style {cg/cmm/coul/long/gpu} is a GPU-enabled version of style
{cg/cmm/coul/long}. See more details below.
The following coefficients must be defined for each pair of atoms
types via the "pair_coeff"_pair_coeff.html command as in the examples
above, or in the data file or restart files read by the
@ -120,18 +109,25 @@ pair_style command.
:line
The styles with a {gpu} suffix are identical to the corresponding
styles without the suffix, except that each processor off-loads its
pairwise calculations to a GPU. Depending on the hardware available
on your system this can provide a speed-up. See "this
section"_doc/Section_accerate.html of the manual for more details.
Styles with a {cuda}, {gpu}, or {opt} suffix are functionally the same
as the corresponding style without the suffix. They have been
optimized to run faster, depending on your available hardware, as
discussed in "this section"_Section_accelerate.html of the manual.
The accelerated styles take the same arguments and should produce the
same results, except for round-off and precision issues.
Additional requirements in your input script to run the styles with a
{gpu} suffix are as follows:
These accelerated styles are part of the "user-cuda", "gpu", and "opt"
packages respectively. They are only enabled if LAMMPS was built with
those packages. See the "Making LAMMPS"_Section_start.html#2_3
section for more info.
The "newton pair"_newton.html setting must be {off} and the "fix
gpu"_fix_gpu.html command must be used. The fix controls the GPU
selection and initialization steps.
You can specify the accelerated styles explicitly in your input script
by including their suffix, or you can use the "-suffix command-line
switch"_Section_start.html#2_6 when you invoke LAMMPS, or you can use
the "suffix"_suffix.html command in your input script.
See "this section"_Section_accelerate.html of the manual for more
instructions on how to use the accelerated styles effectively.
:line
@ -166,12 +162,10 @@ See the "run_style"_run_style.html command for details.
[Restrictions:]
All of the cg/cmm pair styles are part of the "user-cg-cmm"
package. They are only enabled if LAMMPS was built with that package.
All of the cg/cmm pair styles are part of the "user-cg-cmm" package.
The {cg/cmm/coul/long} style also requires the "kspace" package to be
built (which is enabled by default). The styles with a {gpu} suffix
are part of the "gpu" package. They are only enabled if LAMMPS was
built with that package. See the "Making
built (which is enabled by default). They are only enabled if LAMMPS
was built with that package. See the "Making
LAMMPS"_Section_start.html#2_3 section for more info.
[Related commands:]

45
doc/pair_eam.html
View File

@ -27,24 +27,21 @@
</P>
<PRE>pair_style style
</PRE>
<UL><LI>style = <I>eam</I> or <I>eam/alloy</I> or <I>eam/cd</I> or <I>eam/fs</I> or <I>eam/opt</I> or <I>eam/alloy/opt</I> or <I>eam/fs/opt</I>
<UL><LI>style = <I>eam</I> or <I>eam/alloy</I> or <I>eam/cd</I> or <I>eam/fs</I>
</UL>
<P><B>Examples:</B>
</P>
<PRE>pair_style eam
pair_style eam/opt
pair_coeff * * cuu3
pair_coeff 1*3 1*3 niu3.eam
</PRE>
<PRE>pair_style eam/alloy
pair_style eam/alloy/opt
pair_coeff * * ../potentials/NiAlH_jea.eam.alloy Ni Al Ni Ni
</PRE>
<PRE>pair_style eam/cd
pair_coeff * * ../potentials/FeCr.cdeam Fe Cr
</PRE>
<PRE>pair_style eam/fs
pair_style eam/fs/opt
pair_coeff * * NiAlH_jea.eam.fs Ni Al Ni Ni
</PRE>
<P><B>Description:</B>
@ -62,9 +59,6 @@ nature of the EAM potential is a result of the embedding energy term.
Both summations in the formula are over all neighbors J of atom I
within the cutoff distance.
</P>
<P>Style (eam/opt</I> is an optimized version of style <I>eam</I>. See
more details below.
</P>
<P>The cutoff distance and the tabulated values of the functionals F,
rho, and phi are listed in one or more files which are specified by
the <A HREF = "pair_coeff.html">pair_coeff</A> command. These are ASCII text files
@ -183,9 +177,6 @@ above, <I>setfl</I> files contain explicit tabulated values for alloy
interactions. Thus they allow more generality than <I>funcfl</I> files for
modeling alloys.
</P>
<P>Style (eam/alloy/opt</I> is an optimized version of style <I>eam/alloy</I>.
See more details below.
</P>
<P>For style <I>eam/alloy</I>, potential values are read from a file that is
in the DYNAMO multi-element <I>setfl</I> format, except that element names
(Ni, Cu, etc) are added to one of the lines in the file. If the
@ -306,9 +297,6 @@ so that different elements can contribute differently to the total
electron density at an atomic site depending on the identity of the
element at that atomic site.
</P>
<P>Style (eam/fs/opt</I> is an optimized version of style <I>eam/fs</I>. See
more details below.
</P>
<P>The associated <A HREF = "pair_coeff.html">pair_coeff</A> command for style <I>eam/fs</I>
reads a DYNAMO <I>setfl</I> file that has been extended to include
additional rho_alpha_beta arrays of tabulated values. A discussion of
@ -371,10 +359,25 @@ are listed.
</P>
<HR>
<P>The styles with an <I>opt</I> suffix are identical to the corresponding
styles without the suffix, except that it is written in an optimized
fashion for faster CPU execution. See <A HREF = "doc/Section_accerate.html">this
section</A> of the manual for more details.
<P>Styles with a <I>cuda</I>, <I>gpu</I>, or <I>opt</I> suffix are functionally the same
as the corresponding style without the suffix. They have been
optimized to run faster, depending on your available hardware, as
discussed in <A HREF = "Section_accelerate.html">this section</A> of the manual.
The accelerated styles take the same arguments and should produce the
same results, except for round-off and precision issues.
</P>
<P>These accelerated styles are part of the "user-cuda", "gpu", and "opt"
packages respectively. They are only enabled if LAMMPS was built with
those packages. See the <A HREF = "Section_start.html#2_3">Making LAMMPS</A>
section for more info.
</P>
<P>You can specify the accelerated styles explicitly in your input script
by including their suffix, or you can use the <A HREF = "Section_start.html#2_6">-suffix command-line
switch</A> when you invoke LAMMPS, or you can use
the <A HREF = "suffix.html">suffix</A> command in your input script.
</P>
<P>See <A HREF = "Section_accelerate.html">this section</A> of the manual for more
instructions on how to use the accelerated styles effectively.
</P>
<HR>
@ -401,11 +404,9 @@ an input script that reads a restart file.
<P><B>Restrictions:</B>
</P>
<P>All of these styles except those ending in <I>opt</I> and the <I>eam/cd</I>
style are part of the "manybody" package. They are only enabled if
LAMMPS was built with that package (which it is by default). The
styles with an <I>opt</I> suffix are part of the "opt" package. They are
only enabled if LAMMPS was built with that packages. See the <A HREF = "Section_start.html#2_3">Making
<P>All of these styles except the <I>eam/cd</I> style are part of the
"manybody" package. They are only enabled if LAMMPS was built with
that package (which it is by default). See the <A HREF = "Section_start.html#2_3">Making
LAMMPS</A> section for more info.
</P>
<P>The <I>eam/cd</I> style is part of the "user-cd-eam" package and also

45
doc/pair_eam.txt
View File

@ -18,24 +18,21 @@ pair_style eam/fs/opt command :h3
pair_style style :pre
style = {eam} or {eam/alloy} or {eam/cd} or {eam/fs} or {eam/opt} or {eam/alloy/opt} or {eam/fs/opt} :ul
style = {eam} or {eam/alloy} or {eam/cd} or {eam/fs} :ul
[Examples:]
pair_style eam
pair_style eam/opt
pair_coeff * * cuu3
pair_coeff 1*3 1*3 niu3.eam :pre
pair_style eam/alloy
pair_style eam/alloy/opt
pair_coeff * * ../potentials/NiAlH_jea.eam.alloy Ni Al Ni Ni :pre
pair_style eam/cd
pair_coeff * * ../potentials/FeCr.cdeam Fe Cr :pre
pair_style eam/fs
pair_style eam/fs/opt
pair_coeff * * NiAlH_jea.eam.fs Ni Al Ni Ni :pre
[Description:]
@ -53,9 +50,6 @@ nature of the EAM potential is a result of the embedding energy term.
Both summations in the formula are over all neighbors J of atom I
within the cutoff distance.
Style (eam/opt} is an optimized version of style {eam}. See
more details below.
The cutoff distance and the tabulated values of the functionals F,
rho, and phi are listed in one or more files which are specified by
the "pair_coeff"_pair_coeff.html command. These are ASCII text files
@ -174,9 +168,6 @@ above, {setfl} files contain explicit tabulated values for alloy
interactions. Thus they allow more generality than {funcfl} files for
modeling alloys.
Style (eam/alloy/opt} is an optimized version of style {eam/alloy}.
See more details below.
For style {eam/alloy}, potential values are read from a file that is
in the DYNAMO multi-element {setfl} format, except that element names
(Ni, Cu, etc) are added to one of the lines in the file. If the
@ -297,9 +288,6 @@ so that different elements can contribute differently to the total
electron density at an atomic site depending on the identity of the
element at that atomic site.
Style (eam/fs/opt} is an optimized version of style {eam/fs}. See
more details below.
The associated "pair_coeff"_pair_coeff.html command for style {eam/fs}
reads a DYNAMO {setfl} file that has been extended to include
additional rho_alpha_beta arrays of tabulated values. A discussion of
@ -362,10 +350,25 @@ are listed.
:line
The styles with an {opt} suffix are identical to the corresponding
styles without the suffix, except that it is written in an optimized
fashion for faster CPU execution. See "this
section"_doc/Section_accerate.html of the manual for more details.
Styles with a {cuda}, {gpu}, or {opt} suffix are functionally the same
as the corresponding style without the suffix. They have been
optimized to run faster, depending on your available hardware, as
discussed in "this section"_Section_accelerate.html of the manual.
The accelerated styles take the same arguments and should produce the
same results, except for round-off and precision issues.
These accelerated styles are part of the "user-cuda", "gpu", and "opt"
packages respectively. They are only enabled if LAMMPS was built with
those packages. See the "Making LAMMPS"_Section_start.html#2_3
section for more info.
You can specify the accelerated styles explicitly in your input script
by including their suffix, or you can use the "-suffix command-line
switch"_Section_start.html#2_6 when you invoke LAMMPS, or you can use
the "suffix"_suffix.html command in your input script.
See "this section"_Section_accelerate.html of the manual for more
instructions on how to use the accelerated styles effectively.
:line
@ -392,11 +395,9 @@ The eam pair styles can only be used via the {pair} keyword of the
[Restrictions:]
All of these styles except those ending in {opt} and the {eam/cd}
style are part of the "manybody" package. They are only enabled if
LAMMPS was built with that package (which it is by default). The
styles with an {opt} suffix are part of the "opt" package. They are
only enabled if LAMMPS was built with that packages. See the "Making
All of these styles except the {eam/cd} style are part of the
"manybody" package. They are only enabled if LAMMPS was built with
that package (which it is by default). See the "Making
LAMMPS"_Section_start.html#2_3 section for more info.
The {eam/cd} style is part of the "user-cd-eam" package and also

41
doc/pair_gayberne.html
View File

@ -17,10 +17,7 @@
</P>
<PRE>pair_style gayberne gamma upsilon mu cutoff
</PRE>
<PRE>pair_style gayberne/gpu gamma upsilon mu cutoff
</PRE>
<UL><LI>style = <I>gayberne</I> or <I>gayberne/gpu</I>
<LI>gamma = shift for potential minimum (typically 1)
<UL><LI>gamma = shift for potential minimum (typically 1)
<LI>upsilon = exponent for eta orientation-dependent energy function
<LI>mu = exponent for chi orientation-dependent energy function
<LI>cutoff = global cutoff for interactions (distance units)
@ -28,7 +25,6 @@
<P><B>Examples:</B>
</P>
<PRE>pair_style gayberne 1.0 1.0 1.0 10.0
pair_style gayberne/gpu 1.0 1.0 1.0 10.0
pair_coeff * * 1.0 1.7 1.7 3.4 3.4 1.0 1.0 1.0
</PRE>
<P><B>Description:</B>
@ -48,9 +44,6 @@ both particles are spherical, the formula reduces to the usual
Lennard-Jones interaction (see details below for when Gay-Berne treats
a particle as "spherical").
</P>
<P>Style <I>gayberne/gpu</I> is a GPU-enabled version of style <I>gayberne</I>.
See more details below.
</P>
<P>For large uniform molecules it has been shown that the energy
parameters are approximately representable in terms of local contact
curvatures <A HREF = "#Everaers">(Everaers)</A>:
@ -139,18 +132,25 @@ pair_coeff sigma to 1.0 as well.
</P>
<HR>
<P>The styles with a <I>gpu</I> suffix are identical to the corresponding
styles without the suffix, except that each processor off-loads its
pairwise calculations to a GPU. Depending on the hardware available
on your system this can provide a speed-up. See <A HREF = "doc/Section_accerate.html">this
section</A> of the manual for more details.
<P>Styles with a <I>cuda</I>, <I>gpu</I>, or <I>opt</I> suffix are functionally the same
as the corresponding style without the suffix. They have been
optimized to run faster, depending on your available hardware, as
discussed in <A HREF = "Section_accelerate.html">this section</A> of the manual.
The accelerated styles take the same arguments and should produce the
same results, except for round-off and precision issues.
</P>
<P>Additional requirements in your input script to run the styles with a
<I>gpu</I> suffix are as follows:
<P>These accelerated styles are part of the "user-cuda", "gpu", and "opt"
packages respectively. They are only enabled if LAMMPS was built with
those packages. See the <A HREF = "Section_start.html#2_3">Making LAMMPS</A>
section for more info.
</P>
<P>The <A HREF = "newton.html">newton pair</A> setting must be <I>off</I> and the <A HREF = "fix_gpu.html">fix
gpu</A> command must be used. The fix controls the GPU
selection and initialization steps.
<P>You can specify the accelerated styles explicitly in your input script
by including their suffix, or you can use the <A HREF = "Section_start.html#2_6">-suffix command-line
switch</A> when you invoke LAMMPS, or you can use
the <A HREF = "suffix.html">suffix</A> command in your input script.
</P>
<P>See <A HREF = "Section_accelerate.html">this section</A> of the manual for more
instructions on how to use the accelerated styles effectively.
</P>
<HR>
@ -185,9 +185,8 @@ to be specified in an input script that reads a restart file.
<P><B>Restrictions:</B>
</P>
<P>The <I>gayberne</I> style is part of the "asphere" package. The styles
with a <I>gpu</I> suffix are part of the "gpu" package. They are only
enabled if LAMMPS was built with those packages. See the <A HREF = "Section_start.html#2_3">Making
<P>The <I>gayberne</I> style is part of the "asphere" 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>These pair style require that atoms store torque and a quaternion to

38
doc/pair_gayberne.txt
View File

@ -12,9 +12,7 @@ pair_style gayberne/gpu command :h3
[Syntax:]
pair_style gayberne gamma upsilon mu cutoff :pre
pair_style gayberne/gpu gamma upsilon mu cutoff :pre
style = {gayberne} or {gayberne/gpu}
gamma = shift for potential minimum (typically 1)
upsilon = exponent for eta orientation-dependent energy function
mu = exponent for chi orientation-dependent energy function
@ -23,7 +21,6 @@ cutoff = global cutoff for interactions (distance units) :ul
[Examples:]
pair_style gayberne 1.0 1.0 1.0 10.0
pair_style gayberne/gpu 1.0 1.0 1.0 10.0
pair_coeff * * 1.0 1.7 1.7 3.4 3.4 1.0 1.0 1.0 :pre
[Description:]
@ -43,9 +40,6 @@ both particles are spherical, the formula reduces to the usual
Lennard-Jones interaction (see details below for when Gay-Berne treats
a particle as "spherical").
Style {gayberne/gpu} is a GPU-enabled version of style {gayberne}.
See more details below.
For large uniform molecules it has been shown that the energy
parameters are approximately representable in terms of local contact
curvatures "(Everaers)"_#Everaers:
@ -134,18 +128,25 @@ pair_coeff sigma to 1.0 as well.
:line
The styles with a {gpu} suffix are identical to the corresponding
styles without the suffix, except that each processor off-loads its
pairwise calculations to a GPU. Depending on the hardware available
on your system this can provide a speed-up. See "this
section"_doc/Section_accerate.html of the manual for more details.
Styles with a {cuda}, {gpu}, or {opt} suffix are functionally the same
as the corresponding style without the suffix. They have been
optimized to run faster, depending on your available hardware, as
discussed in "this section"_Section_accelerate.html of the manual.
The accelerated styles take the same arguments and should produce the
same results, except for round-off and precision issues.
Additional requirements in your input script to run the styles with a
{gpu} suffix are as follows:
These accelerated styles are part of the "user-cuda", "gpu", and "opt"
packages respectively. They are only enabled if LAMMPS was built with
those packages. See the "Making LAMMPS"_Section_start.html#2_3
section for more info.
The "newton pair"_newton.html setting must be {off} and the "fix
gpu"_fix_gpu.html command must be used. The fix controls the GPU
selection and initialization steps.
You can specify the accelerated styles explicitly in your input script
by including their suffix, or you can use the "-suffix command-line
switch"_Section_start.html#2_6 when you invoke LAMMPS, or you can use
the "suffix"_suffix.html command in your input script.
See "this section"_Section_accelerate.html of the manual for more
instructions on how to use the accelerated styles effectively.
:line
@ -180,9 +181,8 @@ This pair style can only be used via the {pair} keyword of the
[Restrictions:]
The {gayberne} style is part of the "asphere" package. The styles
with a {gpu} suffix are part of the "gpu" package. They are only
enabled if LAMMPS was built with those packages. See the "Making
The {gayberne} style is part of the "asphere" package. It is only
enabled if LAMMPS was built with that package. See the "Making
LAMMPS"_Section_start.html#2_3 section for more info.
These pair style require that atoms store torque and a quaternion to

67
doc/pair_lj.html
View File

@ -31,21 +31,14 @@
</P>
<PRE>pair_style style args
</PRE>
<UL><LI>style = <I>lj/cut</I> or <I>lj/cut/gpu</I> or <I>lj/cut/opt</I> or <I>lj/cut/coul/cut</I> or <I>lj/cut/coul/debye</I> or <I>lj/cut/coul/long</I> or <I>lj/cut/coul/long/tip4p</I>
<UL><LI>style = <I>lj/cut</I> or <I>lj/cut/coul/cut</I> or <I>lj/cut/coul/debye</I> or <I>lj/cut/coul/long</I> or <I>lj/cut/coul/long/tip4p</I>
<LI>args = list of arguments for a particular style
</UL>
<PRE> <I>lj/cut</I> args = cutoff
cutoff = global cutoff for Lennard Jones interactions (distance units)
<I>lj/cut/gpu</I> args = cutoff
cutoff = global cutoff for Lennard Jones interactions (distance units)
<I>lj/cut/opt</I> args = cutoff
cutoff = global cutoff for Lennard Jones interactions (distance units)
<I>lj/cut/coul/cut</I> args = cutoff (cutoff2)
cutoff = global cutoff for LJ (and Coulombic if only 1 arg) (distance units)
cutoff2 = global cutoff for Coulombic (optional) (distance units)
<I>lj/cut/coul/cut/gpu</I> args = cutoff (cutoff2)
cutoff = global cutoff for LJ (and Coulombic if only 1 arg) (distance units)
cutoff2 = global cutoff for Coulombic (optional) (distance units)
<I>lj/cut/coul/debye</I> args = kappa cutoff (cutoff2)
kappa = Debye length (inverse distance units)
cutoff = global cutoff for LJ (and Coulombic if only 1 arg) (distance units)
@ -53,9 +46,6 @@
<I>lj/cut/coul/long</I> args = cutoff (cutoff2)
cutoff = global cutoff for LJ (and Coulombic if only 1 arg) (distance units)
cutoff2 = global cutoff for Coulombic (optional) (distance units)
<I>lj/cut/coul/long/gpu</I> args = cutoff (cutoff2)
cutoff = global cutoff for LJ (and Coulombic if only 1 arg) (distance units)
cutoff2 = global cutoff for Coulombic (optional) (distance units)
<I>lj/cut/coul/long/tip4p</I> args = otype htype btype atype qdist cutoff (cutoff2)
otype,htype = atom types for TIP4P O and H
btype,atype = bond and angle types for TIP4P waters
@ -66,13 +56,10 @@
<P><B>Examples:</B>
</P>
<PRE>pair_style lj/cut 2.5
pair_style lj/cut/gpu 2.5
pair_style lj/cut/opt 2.5
pair_coeff * * 1 1
pair_coeff 1 1 1 1.1 2.8
</PRE>
<PRE>pair_style lj/cut/coul/cut 10.0
pair_style lj/cut/coul/cut/gpu 10.0
pair_style lj/cut/coul/cut 10.0 8.0
pair_coeff * * 100.0 3.0
pair_coeff 1 1 100.0 3.5 9.0
@ -85,7 +72,6 @@ pair_coeff 1 1 1.0 1.5 2.5
pair_coeff 1 1 1.0 1.5 2.5 5.0
</PRE>
<PRE>pair_style lj/cut/coul/long 10.0
pair_style lj/cut/coul/long/gpu 10.0
pair_style lj/cut/coul/long 10.0 8.0
pair_coeff * * 100.0 3.0
pair_coeff 1 1 100.0 3.5 9.0
@ -104,12 +90,6 @@ given by
</CENTER>
<P>Rc is the cutoff.
</P>
<P>Style <I>lj/cut/gpu</I> is a GPU-enabled version of style <I>lj/cut</I>.
See more details below.
</P>
<P>Style <I>lj/cut/opt</I> is an optimized version of style <I>lj/cut</I>. See
more details below.
</P>
<P>Style <I>lj/cut/coul/cut</I> adds a Coulombic pairwise interaction given by
</P>
<CENTER><IMG SRC = "Eqs/pair_coulomb.jpg">
@ -121,9 +101,6 @@ specified in the pair_style command, it is used for both the LJ and
Coulombic terms. If two cutoffs are specified, they are used as
cutoffs for the LJ and Coulombic terms respectively.
</P>
<P>Style <I>lj/cut/coul/cut/gpu</I> is a GPU-enabled version of style
<I>lj/cut/coul/cut</I>. See more details below.
</P>
<P>Style <I>lj/cut/coul/debye</I> adds an additional exp() damping factor
to the Coulombic term, given by
</P>
@ -140,9 +117,6 @@ option. The Coulombic cutoff specified for this style means that
pairwise interactions within this distance are computed directly;
interactions outside that distance are computed in reciprocal space.
</P>
<P>Style <I>lj/cut/coul/long/gpu</I> is a GPU-enabled version of style
<I>lj/cut/coul/long</I>. See more details below.
</P>
<P>Style <I>lj/cut/coul/long/tip4p</I> implements the TIP4P water model of
<A HREF = "#Jorgensen">(Jorgensen)</A>, which introduces a massless site located a
short distance away from the oxygen atom along the bisector of the HOH
@ -189,23 +163,25 @@ Coulombic cutoff specified in the pair_style command.
</P>
<HR>
<P>The styles with an <I>opt</I> suffix are identical to the corresponding
styles without the suffix, except that it is written in an optimized
fashion for faster CPU execution. See <A HREF = "doc/Section_accerate.html">this
section</A> of the manual for more details.
<P>Styles with a <I>cuda</I>, <I>gpu</I>, or <I>opt</I> suffix are functionally the same
as the corresponding style without the suffix. They have been
optimized to run faster, depending on your available hardware, as
discussed in <A HREF = "Section_accelerate.html">this section</A> of the manual.
The accelerated styles take the same arguments and should produce the
same results, except for round-off and precision issues.
</P>
<P>The styles with a <I>gpu</I> suffix are identical to the corresponding
styles without the suffix, except that each processor off-loads its
pairwise calculations to a GPU. Depending on the hardware available
on your system this can provide a speed-up. See <A HREF = "doc/Section_accerate.html">this
section</A> of the manual for more details.
<P>These accelerated styles are part of the "user-cuda", "gpu", and "opt"
packages respectively. They are only enabled if LAMMPS was built with
those packages. See the <A HREF = "Section_start.html#2_3">Making LAMMPS</A>
section for more info.
</P>
<P>Additional requirements in your input script to run the styles with a
<I>gpu</I> suffix are as follows:
<P>You can specify the accelerated styles explicitly in your input script
by including their suffix, or you can use the <A HREF = "Section_start.html#2_6">-suffix command-line
switch</A> when you invoke LAMMPS, or you can use
the <A HREF = "suffix.html">suffix</A> command in your input script.
</P>
<P>The <A HREF = "newton.html">newton pair</A> setting must be <I>off</I> and the <A HREF = "fix_gpu.html">fix
gpu</A> command must be used. The fix controls the GPU
selection and initialization steps.
<P>See <A HREF = "Section_accelerate.html">this section</A> of the manual for more
instructions on how to use the accelerated styles effectively.
</P>
<HR>
@ -246,11 +222,10 @@ See the <A HREF = "run_style.html">run_style</A> command for details.
<P><B>Restrictions:</B>
</P>
<P>The <I>lj/cut/coul/long</I> and <I>lj/cut/coul/long/tip4p</I> styles are part of
the "kspace" package. The styles with an <I>opt</I> or <I>gpu</I> suffix are
part of the "opt" or "gpu" packages. They are only enabled if LAMMPS
was built with those packages. See the <A HREF = "Section_start.html#2_3">Making
LAMMPS</A> section for more info. Note that the
kspace package is installed by default.
the "kspace" package. They are only enabled if LAMMPS was built with
those packages. See the <A HREF = "Section_start.html#2_3">Making LAMMPS</A>
section for more info. Note that the kspace package is installed by
default.
</P>
<P><B>Related commands:</B>
</P>

68
doc/pair_lj.txt
View File

@ -20,21 +20,13 @@ pair_style lj/cut/coul/long/tip4p command :h3
pair_style style args :pre
style = {lj/cut} or {lj/cut/gpu} or {lj/cut/opt} or {lj/cut/coul/cut} \
or {lj/cut/coul/debye} or {lj/cut/coul/long} or {lj/cut/coul/long/tip4p}
style = {lj/cut} or {lj/cut/coul/cut} or {lj/cut/coul/debye} or {lj/cut/coul/long} or {lj/cut/coul/long/tip4p}
args = list of arguments for a particular style :ul
{lj/cut} args = cutoff
cutoff = global cutoff for Lennard Jones interactions (distance units)
{lj/cut/gpu} args = cutoff
cutoff = global cutoff for Lennard Jones interactions (distance units)
{lj/cut/opt} args = cutoff
cutoff = global cutoff for Lennard Jones interactions (distance units)
{lj/cut/coul/cut} args = cutoff (cutoff2)
cutoff = global cutoff for LJ (and Coulombic if only 1 arg) (distance units)
cutoff2 = global cutoff for Coulombic (optional) (distance units)
{lj/cut/coul/cut/gpu} args = cutoff (cutoff2)
cutoff = global cutoff for LJ (and Coulombic if only 1 arg) (distance units)
cutoff2 = global cutoff for Coulombic (optional) (distance units)
{lj/cut/coul/debye} args = kappa cutoff (cutoff2)
kappa = Debye length (inverse distance units)
cutoff = global cutoff for LJ (and Coulombic if only 1 arg) (distance units)
@ -42,9 +34,6 @@ args = list of arguments for a particular style :ul
{lj/cut/coul/long} args = cutoff (cutoff2)
cutoff = global cutoff for LJ (and Coulombic if only 1 arg) (distance units)
cutoff2 = global cutoff for Coulombic (optional) (distance units)
{lj/cut/coul/long/gpu} args = cutoff (cutoff2)
cutoff = global cutoff for LJ (and Coulombic if only 1 arg) (distance units)
cutoff2 = global cutoff for Coulombic (optional) (distance units)
{lj/cut/coul/long/tip4p} args = otype htype btype atype qdist cutoff (cutoff2)
otype,htype = atom types for TIP4P O and H
btype,atype = bond and angle types for TIP4P waters
@ -55,13 +44,10 @@ args = list of arguments for a particular style :ul
[Examples:]
pair_style lj/cut 2.5
pair_style lj/cut/gpu 2.5
pair_style lj/cut/opt 2.5
pair_coeff * * 1 1
pair_coeff 1 1 1 1.1 2.8 :pre
pair_style lj/cut/coul/cut 10.0
pair_style lj/cut/coul/cut/gpu 10.0
pair_style lj/cut/coul/cut 10.0 8.0
pair_coeff * * 100.0 3.0
pair_coeff 1 1 100.0 3.5 9.0
@ -74,7 +60,6 @@ pair_coeff 1 1 1.0 1.5 2.5
pair_coeff 1 1 1.0 1.5 2.5 5.0 :pre
pair_style lj/cut/coul/long 10.0
pair_style lj/cut/coul/long/gpu 10.0
pair_style lj/cut/coul/long 10.0 8.0
pair_coeff * * 100.0 3.0
pair_coeff 1 1 100.0 3.5 9.0 :pre
@ -93,12 +78,6 @@ given by
Rc is the cutoff.
Style {lj/cut/gpu} is a GPU-enabled version of style {lj/cut}.
See more details below.
Style {lj/cut/opt} is an optimized version of style {lj/cut}. See
more details below.
Style {lj/cut/coul/cut} adds a Coulombic pairwise interaction given by
:c,image(Eqs/pair_coulomb.jpg)
@ -110,9 +89,6 @@ specified in the pair_style command, it is used for both the LJ and
Coulombic terms. If two cutoffs are specified, they are used as
cutoffs for the LJ and Coulombic terms respectively.
Style {lj/cut/coul/cut/gpu} is a GPU-enabled version of style
{lj/cut/coul/cut}. See more details below.
Style {lj/cut/coul/debye} adds an additional exp() damping factor
to the Coulombic term, given by
@ -129,9 +105,6 @@ option. The Coulombic cutoff specified for this style means that
pairwise interactions within this distance are computed directly;
interactions outside that distance are computed in reciprocal space.
Style {lj/cut/coul/long/gpu} is a GPU-enabled version of style
{lj/cut/coul/long}. See more details below.
Style {lj/cut/coul/long/tip4p} implements the TIP4P water model of
"(Jorgensen)"_#Jorgensen, which introduces a massless site located a
short distance away from the oxygen atom along the bisector of the HOH
@ -178,23 +151,25 @@ Coulombic cutoff specified in the pair_style command.
:line
The styles with an {opt} suffix are identical to the corresponding
styles without the suffix, except that it is written in an optimized
fashion for faster CPU execution. See "this
section"_doc/Section_accerate.html of the manual for more details.
Styles with a {cuda}, {gpu}, or {opt} suffix are functionally the same
as the corresponding style without the suffix. They have been
optimized to run faster, depending on your available hardware, as
discussed in "this section"_Section_accelerate.html of the manual.
The accelerated styles take the same arguments and should produce the
same results, except for round-off and precision issues.
The styles with a {gpu} suffix are identical to the corresponding
styles without the suffix, except that each processor off-loads its
pairwise calculations to a GPU. Depending on the hardware available
on your system this can provide a speed-up. See "this
section"_doc/Section_accerate.html of the manual for more details.
These accelerated styles are part of the "user-cuda", "gpu", and "opt"
packages respectively. They are only enabled if LAMMPS was built with
those packages. See the "Making LAMMPS"_Section_start.html#2_3
section for more info.
Additional requirements in your input script to run the styles with a
{gpu} suffix are as follows:
You can specify the accelerated styles explicitly in your input script
by including their suffix, or you can use the "-suffix command-line
switch"_Section_start.html#2_6 when you invoke LAMMPS, or you can use
the "suffix"_suffix.html command in your input script.
The "newton pair"_newton.html setting must be {off} and the "fix
gpu"_fix_gpu.html command must be used. The fix controls the GPU
selection and initialization steps.
See "this section"_Section_accelerate.html of the manual for more
instructions on how to use the accelerated styles effectively.
:line
@ -235,11 +210,10 @@ See the "run_style"_run_style.html command for details.
[Restrictions:]
The {lj/cut/coul/long} and {lj/cut/coul/long/tip4p} styles are part of
the "kspace" package. The styles with an {opt} or {gpu} suffix are
part of the "opt" or "gpu" packages. They are only enabled if LAMMPS
was built with those packages. See the "Making
LAMMPS"_Section_start.html#2_3 section for more info. Note that the
kspace package is installed by default.
the "kspace" package. They are only enabled if LAMMPS was built with
those packages. See the "Making LAMMPS"_Section_start.html#2_3
section for more info. Note that the kspace package is installed by
default.
[Related commands:]

42
doc/pair_lj96_cut.html
View File

@ -15,15 +15,13 @@
</H3>
<P><B>Syntax:</B>
</P>
<PRE>pair_style style cutoff
<PRE>pair_style lj96/cut cutoff
</PRE>
<UL><LI>style = <I>lj96/cut</I> or <I>lj96/cut/gpu</I>
<LI>cutoff = global cutoff for lj96/cut interactions (distance units)
<UL><LI>cutoff = global cutoff for lj96/cut interactions (distance units)
</UL>
<P><B>Examples:</B>
</P>
<PRE>pair_style lj96/cut 2.5
pair_style lj96/cut/gpu 2.5
pair_coeff * * 1.0 1.0 4.0
pair_coeff 1 1 1.0 1.0
</PRE>
@ -36,9 +34,6 @@ of the standard 12/6 potential, given by
</CENTER>
<P>Rc is the cutoff.
</P>
<P>Style <I>lj96/cut/gpu</I> is a GPU-enabled version of style <I>lj96/cut</I>.
See more details below.
</P>
<P>The following coefficients must be defined for each pair of atoms
types via the <A HREF = "pair_coeff.html">pair_coeff</A> command as in the examples
above, or in the data file or restart files read by the
@ -54,18 +49,25 @@ cutoff specified in the pair_style command is used.
</P>
<HR>
<P>The styles with a <I>gpu</I> suffix are identical to the corresponding
styles without the suffix, except that each processor off-loads its
pairwise calculations to a GPU. Depending on the hardware available
on your system this can provide a speed-up. See <A HREF = "doc/Section_accerate.html">this
section</A> of the manual for more details.
<P>Styles with a <I>cuda</I>, <I>gpu</I>, or <I>opt</I> suffix are functionally the same
as the corresponding style without the suffix. They have been
optimized to run faster, depending on your available hardware, as
discussed in <A HREF = "Section_accelerate.html">this section</A> of the manual.
The accelerated styles take the same arguments and should produce the
same results, except for round-off and precision issues.
</P>
<P>Additional requirements in your input script to run the styles with a
<I>gpu</I> suffix are as follows:
<P>These accelerated styles are part of the "user-cuda", "gpu", and "opt"
packages respectively. They are only enabled if LAMMPS was built with
those packages. See the <A HREF = "Section_start.html#2_3">Making LAMMPS</A>
section for more info.
</P>
<P>The <A HREF = "newton.html">newton pair</A> setting must be <I>off</I> and the <A HREF = "fix_gpu.html">fix
gpu</A> command must be used. The fix controls the GPU
selection and initialization steps.
<P>You can specify the accelerated styles explicitly in your input script
by including their suffix, or you can use the <A HREF = "Section_start.html#2_6">-suffix command-line
switch</A> when you invoke LAMMPS, or you can use
the <A HREF = "suffix.html">suffix</A> command in your input script.
</P>
<P>See <A HREF = "Section_accelerate.html">this section</A> of the manual for more
instructions on how to use the accelerated styles effectively.
</P>
<HR>
@ -98,11 +100,7 @@ details.
</P>
<HR>
<P><B>Restrictions:</B>
</P>
<P>The styles with a <I>gpu</I> suffix are part of the "gpu" package. They
are only enabled if LAMMPS was built with those packages. See the
<A HREF = "Section_start.html#2_3">Making LAMMPS</A> section for more info.
<P><B>Restrictions:</B> none
</P>
<P><B>Related commands:</B>
</P>

40
doc/pair_lj96_cut.txt
View File

@ -11,15 +11,13 @@ pair_style lj96/cut/gpu command :h3
[Syntax:]
pair_style style cutoff :pre
pair_style lj96/cut cutoff :pre
style = {lj96/cut} or {lj96/cut/gpu}
cutoff = global cutoff for lj96/cut interactions (distance units) :ul
[Examples:]
pair_style lj96/cut 2.5
pair_style lj96/cut/gpu 2.5
pair_coeff * * 1.0 1.0 4.0
pair_coeff 1 1 1.0 1.0 :pre
@ -32,9 +30,6 @@ of the standard 12/6 potential, given by
Rc is the cutoff.
Style {lj96/cut/gpu} is a GPU-enabled version of style {lj96/cut}.
See more details below.
The following coefficients must be defined for each pair of atoms
types via the "pair_coeff"_pair_coeff.html command as in the examples
above, or in the data file or restart files read by the
@ -50,18 +45,25 @@ cutoff specified in the pair_style command is used.
:line
The styles with a {gpu} suffix are identical to the corresponding
styles without the suffix, except that each processor off-loads its
pairwise calculations to a GPU. Depending on the hardware available
on your system this can provide a speed-up. See "this
section"_doc/Section_accerate.html of the manual for more details.
Styles with a {cuda}, {gpu}, or {opt} suffix are functionally the same
as the corresponding style without the suffix. They have been
optimized to run faster, depending on your available hardware, as
discussed in "this section"_Section_accelerate.html of the manual.
The accelerated styles take the same arguments and should produce the
same results, except for round-off and precision issues.
Additional requirements in your input script to run the styles with a
{gpu} suffix are as follows:
These accelerated styles are part of the "user-cuda", "gpu", and "opt"
packages respectively. They are only enabled if LAMMPS was built with
those packages. See the "Making LAMMPS"_Section_start.html#2_3
section for more info.
The "newton pair"_newton.html setting must be {off} and the "fix
gpu"_fix_gpu.html command must be used. The fix controls the GPU
selection and initialization steps.
You can specify the accelerated styles explicitly in your input script
by including their suffix, or you can use the "-suffix command-line
switch"_Section_start.html#2_6 when you invoke LAMMPS, or you can use
the "suffix"_suffix.html command in your input script.
See "this section"_Section_accelerate.html of the manual for more
instructions on how to use the accelerated styles effectively.
:line
@ -94,11 +96,7 @@ details.
:line
[Restrictions:]
The styles with a {gpu} suffix are part of the "gpu" package. They
are only enabled if LAMMPS was built with those packages. See the
"Making LAMMPS"_Section_start.html#2_3 section for more info.
[Restrictions:] none
[Related commands:]

38
doc/pair_lj_expand.html
View File

@ -17,8 +17,6 @@
</P>
<PRE>pair_style lj/expand cutoff
</PRE>
<PRE>pair_style lj/expand/gpu cutoff
</PRE>
<UL><LI>cutoff = global cutoff for lj/expand interactions (distance units)
</UL>
<P><B>Examples:</B>
@ -53,23 +51,27 @@ commands, or by mixing as described below:
<P>The delta values can be positive or negative. The last coefficient is
optional. If not specified, the global LJ cutoff is used.
</P>
<P>Style <I>lj/expand/gpu</I> is a GPU-enabled version of style <I>lj/expand</I>.
See more details below.
</P>
<HR>
<P>The styles with a <I>gpu</I> suffix are identical to the corresponding
styles without the suffix, except that each processor off-loads its
pairwise calculations to a GPU. Depending on the hardware available
on your system this can provide a speed-up. See <A HREF = "doc/Section_accerate.html">this
section</A> of the manual for more details.
<P>Styles with a <I>cuda</I>, <I>gpu</I>, or <I>opt</I> suffix are functionally the same
as the corresponding style without the suffix. They have been
optimized to run faster, depending on your available hardware, as
discussed in <A HREF = "Section_accelerate.html">this section</A> of the manual.
The accelerated styles take the same arguments and should produce the
same results, except for round-off and precision issues.
</P>
<P>Additional requirements in your input script to run the styles with a
<I>gpu</I> suffix are as follows:
<P>These accelerated styles are part of the "user-cuda", "gpu", and "opt"
packages respectively. They are only enabled if LAMMPS was built with
those packages. See the <A HREF = "Section_start.html#2_3">Making LAMMPS</A>
section for more info.
</P>
<P>The <A HREF = "newton.html">newton pair</A> setting must be <I>off</I> and the <A HREF = "fix_gpu.html">fix
gpu</A> command must be used. The fix controls the GPU
selection and initialization steps.
<P>You can specify the accelerated styles explicitly in your input script
by including their suffix, or you can use the <A HREF = "Section_start.html#2_6">-suffix command-line
switch</A> when you invoke LAMMPS, or you can use
the <A HREF = "suffix.html">suffix</A> command in your input script.
</P>
<P>See <A HREF = "Section_accelerate.html">this section</A> of the manual for more
instructions on how to use the accelerated styles effectively.
</P>
<HR>
@ -102,11 +104,7 @@ to be specified in an input script that reads a restart file.
</P>
<HR>
<P><B>Restrictions:</B>
</P>
<P>The styles with a <I>gpu</I> suffix are part of the "gpu" package. They
are only enabled if LAMMPS was built with those packages. See the
<A HREF = "Section_start.html#2_3">Making LAMMPS</A> section for more info.
<P><B>Restrictions:</B> none
</P>
<P><B>Related commands:</B>
</P>

37
doc/pair_lj_expand.txt
View File

@ -12,7 +12,6 @@ pair_style lj/expand/gpu command :h3
[Syntax:]
pair_style lj/expand cutoff :pre
pair_style lj/expand/gpu cutoff :pre
cutoff = global cutoff for lj/expand interactions (distance units) :ul
@ -48,23 +47,27 @@ cutoff (distance units) :ul
The delta values can be positive or negative. The last coefficient is
optional. If not specified, the global LJ cutoff is used.
Style {lj/expand/gpu} is a GPU-enabled version of style {lj/expand}.
See more details below.
:line
The styles with a {gpu} suffix are identical to the corresponding
styles without the suffix, except that each processor off-loads its
pairwise calculations to a GPU. Depending on the hardware available
on your system this can provide a speed-up. See "this
section"_doc/Section_accerate.html of the manual for more details.
Styles with a {cuda}, {gpu}, or {opt} suffix are functionally the same
as the corresponding style without the suffix. They have been
optimized to run faster, depending on your available hardware, as
discussed in "this section"_Section_accelerate.html of the manual.
The accelerated styles take the same arguments and should produce the
same results, except for round-off and precision issues.
Additional requirements in your input script to run the styles with a
{gpu} suffix are as follows:
These accelerated styles are part of the "user-cuda", "gpu", and "opt"
packages respectively. They are only enabled if LAMMPS was built with
those packages. See the "Making LAMMPS"_Section_start.html#2_3
section for more info.
The "newton pair"_newton.html setting must be {off} and the "fix
gpu"_fix_gpu.html command must be used. The fix controls the GPU
selection and initialization steps.
You can specify the accelerated styles explicitly in your input script
by including their suffix, or you can use the "-suffix command-line
switch"_Section_start.html#2_6 when you invoke LAMMPS, or you can use
the "suffix"_suffix.html command in your input script.
See "this section"_Section_accelerate.html of the manual for more
instructions on how to use the accelerated styles effectively.
:line
@ -97,11 +100,7 @@ This pair style can only be used via the {pair} keyword of the
:line
[Restrictions:]
The styles with a {gpu} suffix are part of the "gpu" package. They
are only enabled if LAMMPS was built with those packages. See the
"Making LAMMPS"_Section_start.html#2_3 section for more info.
[Restrictions:] none
[Related commands:]

48
doc/pair_morse.html
View File

@ -19,16 +19,11 @@
</P>
<PRE>pair_style morse cutoff
</PRE>
<PRE>pair_style morse/gpu cutoff
</PRE>
<PRE>pair_style morse/opt cutoff
</PRE>
<UL><LI>cutoff = global cutoff for Morse interactions (distance units)
</UL>
<P><B>Examples:</B>
</P>
<PRE>pair_style morse 2.5
pair_style morse/opt 2.5
pair_coeff * * 100.0 2.0 1.5
pair_coeff 1 1 100.0 2.0 1.5 3.0
</PRE>
@ -54,31 +49,27 @@ commands:
<P>The last coefficient is optional. If not specified, the global morse
cutoff is used.
</P>
<P>Style (morse/opt</I> is an optimized version of style <I>eam</I>. See
more details below.
</P>
<P>Style <I>morse/gpu</I> is a GPU-enabled version of style <I>morse</I>.
See more details below.
</P>
<HR>
<P>The styles with an <I>opt</I> suffix are identical to the corresponding
styles without the suffix, except that it is written in an optimized
fashion for faster CPU execution. See <A HREF = "doc/Section_accerate.html">this
section</A> of the manual for more details.
<P>Styles with a <I>cuda</I>, <I>gpu</I>, or <I>opt</I> suffix are functionally the same
as the corresponding style without the suffix. They have been
optimized to run faster, depending on your available hardware, as
discussed in <A HREF = "Section_accelerate.html">this section</A> of the manual.
The accelerated styles take the same arguments and should produce the
same results, except for round-off and precision issues.
</P>
<P>The styles with a <I>gpu</I> suffix are identical to the corresponding
styles without the suffix, except that each processor off-loads its
pairwise calculations to a GPU. Depending on the hardware available
on your system this can provide a speed-up. See <A HREF = "doc/Section_accerate.html">this
section</A> of the manual for more details.
<P>These accelerated styles are part of the "user-cuda", "gpu", and "opt"
packages respectively. They are only enabled if LAMMPS was built with
those packages. See the <A HREF = "Section_start.html#2_3">Making LAMMPS</A>
section for more info.
</P>
<P>Additional requirements in your input script to run the styles with a
<I>gpu</I> suffix are as follows:
<P>You can specify the accelerated styles explicitly in your input script
by including their suffix, or you can use the <A HREF = "Section_start.html#2_6">-suffix command-line
switch</A> when you invoke LAMMPS, or you can use
the <A HREF = "suffix.html">suffix</A> command in your input script.
</P>
<P>The <A HREF = "newton.html">newton pair</A> setting must be <I>off</I> and the <A HREF = "fix_gpu.html">fix
gpu</A> command must be used. The fix controls the GPU
selection and initialization steps.
<P>See <A HREF = "Section_accelerate.html">this section</A> of the manual for more
instructions on how to use the accelerated styles effectively.
</P>
<HR>
@ -107,12 +98,7 @@ to be specified in an input script that reads a restart file.
</P>
<HR>
<P><B>Restrictions:</B>
</P>
<P>The styles with an <I>opt</I> or <I>gpu</I> suffix are part of the "opt" or
"gpu" packages. They are only enabled if LAMMPS was built with those
packages. See the <A HREF = "Section_start.html#2_3">Making LAMMPS</A> section for
more info.
<P><B>Restrictions:</B> none
</P>
<P><B>Related commands:</B>
</P>

46
doc/pair_morse.txt
View File

@ -13,15 +13,12 @@ pair_style morse/opt command :h3
[Syntax:]
pair_style morse cutoff :pre
pair_style morse/gpu cutoff :pre
pair_style morse/opt cutoff :pre
cutoff = global cutoff for Morse interactions (distance units) :ul
[Examples:]
pair_style morse 2.5
pair_style morse/opt 2.5
pair_coeff * * 100.0 2.0 1.5
pair_coeff 1 1 100.0 2.0 1.5 3.0 :pre
@ -47,31 +44,27 @@ cutoff (distance units) :ul
The last coefficient is optional. If not specified, the global morse
cutoff is used.
Style (morse/opt} is an optimized version of style {eam}. See
more details below.
Style {morse/gpu} is a GPU-enabled version of style {morse}.
See more details below.
:line
The styles with an {opt} suffix are identical to the corresponding
styles without the suffix, except that it is written in an optimized
fashion for faster CPU execution. See "this
section"_doc/Section_accerate.html of the manual for more details.
Styles with a {cuda}, {gpu}, or {opt} suffix are functionally the same
as the corresponding style without the suffix. They have been
optimized to run faster, depending on your available hardware, as
discussed in "this section"_Section_accelerate.html of the manual.
The accelerated styles take the same arguments and should produce the
same results, except for round-off and precision issues.
The styles with a {gpu} suffix are identical to the corresponding
styles without the suffix, except that each processor off-loads its
pairwise calculations to a GPU. Depending on the hardware available
on your system this can provide a speed-up. See "this
section"_doc/Section_accerate.html of the manual for more details.
These accelerated styles are part of the "user-cuda", "gpu", and "opt"
packages respectively. They are only enabled if LAMMPS was built with
those packages. See the "Making LAMMPS"_Section_start.html#2_3
section for more info.
Additional requirements in your input script to run the styles with a
{gpu} suffix are as follows:
You can specify the accelerated styles explicitly in your input script
by including their suffix, or you can use the "-suffix command-line
switch"_Section_start.html#2_6 when you invoke LAMMPS, or you can use
the "suffix"_suffix.html command in your input script.
The "newton pair"_newton.html setting must be {off} and the "fix
gpu"_fix_gpu.html command must be used. The fix controls the GPU
selection and initialization steps.
See "this section"_Section_accelerate.html of the manual for more
instructions on how to use the accelerated styles effectively.
:line
@ -100,12 +93,7 @@ These pair styles can only be used via the {pair} keyword of the
:line
[Restrictions:]
The styles with an {opt} or {gpu} suffix are part of the "opt" or
"gpu" packages. They are only enabled if LAMMPS was built with those
packages. See the "Making LAMMPS"_Section_start.html#2_3 section for
more info.
[Restrictions:] none
[Related commands:]

41
doc/pair_resquared.html
View File

@ -15,15 +15,13 @@
</H3>
<P><B>Syntax:</B>
</P>
<PRE>pair_style style cutoff
<PRE>pair_style resquared cutoff
</PRE>
<UL><LI>style = <I>resquared</I> or <I>resquared/gpu</I>
<LI>cutoff = global cutoff for interactions (distance units)
<UL><LI>cutoff = global cutoff for interactions (distance units)
</UL>
<P><B>Examples:</B>
</P>
<PRE>pair_style resquared 10.0
pair_style resquared/gpu 10.0
pair_coeff * * 1.0 1.0 1.7 3.4 3.4 1.0 1.0 1.0
</PRE>
<P><B>Description:</B>
@ -36,9 +34,6 @@ of small spheres of size sigma. LJ particles are a single sphere of
size sigma. The distinction is made to allow the pair style to make
efficient calculations of ellipsoid/solvent interactions.
</P>
<P>Style <I>resquared/gpu</I> is a GPU-enabled version of style <I>resquared</I>.
See more details below.
</P>
<P>Details for the equations used are given in the references below and
in <A HREF = "PDF/pair_resquared_extra.pdf">this supplementary document</A>.
</P>
@ -150,18 +145,25 @@ specified in the pair_style command is used.
</P>
<HR>
<P>The styles with a <I>gpu</I> suffix are identical to the corresponding
styles without the suffix, except that each processor off-loads its
pairwise calculations to a GPU. Depending on the hardware available
on your system this can provide a speed-up. See <A HREF = "doc/Section_accerate.html">this
section</A> of the manual for more details.
<P>Styles with a <I>cuda</I>, <I>gpu</I>, or <I>opt</I> suffix are functionally the same
as the corresponding style without the suffix. They have been
optimized to run faster, depending on your available hardware, as
discussed in <A HREF = "Section_accelerate.html">this section</A> of the manual.
The accelerated styles take the same arguments and should produce the
same results, except for round-off and precision issues.
</P>
<P>Additional requirements in your input script to run the styles with a
<I>gpu</I> suffix are as follows:
<P>These accelerated styles are part of the "user-cuda", "gpu", and "opt"
packages respectively. They are only enabled if LAMMPS was built with
those packages. See the <A HREF = "Section_start.html#2_3">Making LAMMPS</A>
section for more info.
</P>
<P>The <A HREF = "newton.html">newton pair</A> setting must be <I>off</I> and the <A HREF = "fix_gpu.html">fix
gpu</A> command must be used. The fix controls the GPU
selection and initialization steps.
<P>You can specify the accelerated styles explicitly in your input script
by including their suffix, or you can use the <A HREF = "Section_start.html#2_6">-suffix command-line
switch</A> when you invoke LAMMPS, or you can use
the <A HREF = "suffix.html">suffix</A> command in your input script.
</P>
<P>See <A HREF = "Section_accelerate.html">this section</A> of the manual for more
instructions on how to use the accelerated styles effectively.
</P>
<HR>
@ -203,9 +205,8 @@ command</A>.
<P><B>Restrictions:</B>
</P>
<P>This style is part of the "asphere" package. The styles with a <I>gpu</I>
suffix are part of the "gpu" package. They are only enabled if LAMMPS
was built with those packages. See the <A HREF = "Section_start.html#2_3">Making
<P>This style is part of the "asphere" 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>This pair style requires that atoms be ellipsoids as defined by the

39
doc/pair_resquared.txt
View File

@ -11,15 +11,13 @@ pair_style resquared/gpu command :h3
[Syntax:]
pair_style style cutoff :pre
pair_style resquared cutoff :pre
style = {resquared} or {resquared/gpu}
cutoff = global cutoff for interactions (distance units) :ul
[Examples:]
pair_style resquared 10.0
pair_style resquared/gpu 10.0
pair_coeff * * 1.0 1.0 1.7 3.4 3.4 1.0 1.0 1.0 :pre
[Description:]
@ -32,9 +30,6 @@ of small spheres of size sigma. LJ particles are a single sphere of
size sigma. The distinction is made to allow the pair style to make
efficient calculations of ellipsoid/solvent interactions.
Style {resquared/gpu} is a GPU-enabled version of style {resquared}.
See more details below.
Details for the equations used are given in the references below and
in "this supplementary document"_PDF/pair_resquared_extra.pdf.
@ -146,18 +141,25 @@ specified in the pair_style command is used.
:line
The styles with a {gpu} suffix are identical to the corresponding
styles without the suffix, except that each processor off-loads its
pairwise calculations to a GPU. Depending on the hardware available
on your system this can provide a speed-up. See "this
section"_doc/Section_accerate.html of the manual for more details.
Styles with a {cuda}, {gpu}, or {opt} suffix are functionally the same
as the corresponding style without the suffix. They have been
optimized to run faster, depending on your available hardware, as
discussed in "this section"_Section_accelerate.html of the manual.
The accelerated styles take the same arguments and should produce the
same results, except for round-off and precision issues.
Additional requirements in your input script to run the styles with a
{gpu} suffix are as follows:
These accelerated styles are part of the "user-cuda", "gpu", and "opt"
packages respectively. They are only enabled if LAMMPS was built with
those packages. See the "Making LAMMPS"_Section_start.html#2_3
section for more info.
The "newton pair"_newton.html setting must be {off} and the "fix
gpu"_fix_gpu.html command must be used. The fix controls the GPU
selection and initialization steps.
You can specify the accelerated styles explicitly in your input script
by including their suffix, or you can use the "-suffix command-line
switch"_Section_start.html#2_6 when you invoke LAMMPS, or you can use
the "suffix"_suffix.html command in your input script.
See "this section"_Section_accelerate.html of the manual for more
instructions on how to use the accelerated styles effectively.
:line
@ -199,9 +201,8 @@ command"_run_style.html.
[Restrictions:]
This style is part of the "asphere" package. The styles with a {gpu}
suffix are part of the "gpu" package. They are only enabled if LAMMPS
was built with those packages. See the "Making
This style is part of the "asphere" package. It is only enabled if
LAMMPS was built with that package. See the "Making
LAMMPS"_Section_start.html#2_3 section for more info.
This pair style requires that atoms be ellipsoids as defined by the