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7
doc/Section_accelerate.html
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@ -106,6 +106,13 @@ to 20% savings.
<H4><A NAME = "10_2"></A>10.2 GPU package <H4><A NAME = "10_2"></A>10.2 GPU package
</H4> </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>The GPU package was developed by Mike Brown at ORNL.
</P> </P>
<P>A few LAMMPS <A HREF = "pair_style.html">pair styles</A> can be run on graphical <P>A few LAMMPS <A HREF = "pair_style.html">pair styles</A> can be run on graphical

9
doc/Section_accelerate.txt
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@ -102,6 +102,15 @@ to 20% savings.
10.2 GPU package :h4,link(10_2) 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. The GPU package was developed by Mike Brown at ORNL.
A few LAMMPS "pair styles"_pair_style.html can be run on graphical A few LAMMPS "pair styles"_pair_style.html can be run on graphical

43
doc/kspace_style.html
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@ -76,9 +76,6 @@ long-range potentials.
<P>Currently, only the <I>ewald/n</I> style can be used with non-orthogonal <P>Currently, only the <I>ewald/n</I> style can be used with non-orthogonal
(triclinic symmetry) simulation boxes. (triclinic symmetry) simulation boxes.
</P> </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> <HR>
<P>When a kspace style is used, a pair style that includes the <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> </P>
<HR> <HR>
<P>The <I>pppm/gpu/single</I> style performs single precision charge <P>Styles with a <I>cuda</I>, <I>gpu/single</I>, <I>gpu/double</I>, or <I>opt</I> suffix are
assignment and force interpolation calculations on the GPU. The functionally the same as the corresponding style without the suffix.
<I>pppm/gpu/double</I> style performs the mesh calculations on the GPU in They have been optimized to run faster, depending on your available
double precision. In both cases, FFT solves are calculated on the CPU. hardware, as discussed in <A HREF = "Section_accelerate.html">this section</A> of
If either <I>pppm/gpu/single</I> or <I>pppm/gpu/double</I> are used with a the manual. The accelerated styles take the same arguments and should
GPU-enabled pair style, part of the PPPM calculation can be performed produce the same results, except for round-off and precision issues.
concurrently on the GPU while other calculations for non-bonded and
bonded force calculation are performed on the CPU.
</P> </P>
<P>See <A HREF = "doc/Section_accerate.html">this section</A> of the manual for more <P>More specifically, the <I>pppm/gpu/single</I> style performs single
details. 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>
<P>Additional requirements in your input script to run with GPU-enabled <P>These accelerated styles are part of the "user-cuda", "gpu", and "opt"
PPPM styles are as follows: 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>
<P>The <A HREF = "fix_gpu.html">fix gpu</A> command must be used. The fix controls the <P>See <A HREF = "Section_accelerate.html">this section</A> of the manual for more
GPU selection and initialization steps. instructions on how to use the accelerated styles effectively.
</P> </P>
<P><B>Restrictions:</B> <P><B>Restrictions:</B>
</P> </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 enabled if LAMMPS was built with that package. See the <A HREF = "Section_start.html#2_3">Making
LAMMPS</A> section for more info. LAMMPS</A> section for more info.
</P> </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 <P>When using a long-range pairwise TIP4P potential, you must use kspace
style <I>pppm/tip4p</I> and vice versa. style <I>pppm/tip4p</I> and vice versa.
</P> </P>

43
doc/kspace_style.txt
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@ -71,9 +71,6 @@ long-range potentials.
Currently, only the {ewald/n} style can be used with non-orthogonal Currently, only the {ewald/n} style can be used with non-orthogonal
(triclinic symmetry) simulation boxes. (triclinic symmetry) simulation boxes.
The {pppm/gpu/single} and {pppm/gpu/double} styles are GPU-enabled
version of {pppm}. See more details below.
:line :line
When a kspace style is used, a pair style that includes the 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 :line
The {pppm/gpu/single} style performs single precision charge Styles with a {cuda}, {gpu/single}, {gpu/double}, or {opt} suffix are
assignment and force interpolation calculations on the GPU. The functionally the same as the corresponding style without the suffix.
{pppm/gpu/double} style performs the mesh calculations on the GPU in They have been optimized to run faster, depending on your available
double precision. In both cases, FFT solves are calculated on the CPU. hardware, as discussed in "this section"_Section_accelerate.html of
If either {pppm/gpu/single} or {pppm/gpu/double} are used with a the manual. The accelerated styles take the same arguments and should
GPU-enabled pair style, part of the PPPM calculation can be performed produce the same results, except for round-off and precision issues.
concurrently on the GPU while other calculations for non-bonded and
bonded force calculation are performed on the CPU.
See "this section"_doc/Section_accerate.html of the manual for more More specifically, the {pppm/gpu/single} style performs single
details. 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 These accelerated styles are part of the "user-cuda", "gpu", and "opt"
PPPM styles are as follows: 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 See "this section"_Section_accelerate.html of the manual for more
GPU selection and initialization steps. instructions on how to use the accelerated styles effectively.
[Restrictions:] [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 enabled if LAMMPS was built with that package. See the "Making
LAMMPS"_Section_start.html#2_3 section for more info. 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 When using a long-range pairwise TIP4P potential, you must use kspace
style {pppm/tip4p} and vice versa. style {pppm/tip4p} and vice versa.

55
doc/pair_charmm.html
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@ -23,7 +23,7 @@
</P> </P>
<PRE>pair_style style args <PRE>pair_style style args
</PRE> </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 <LI>args = list of arguments for a particular style
</UL> </UL>
<PRE> <I>lj/charmm/coul/charmm</I> args = inner outer (inner2) (outer2) <PRE> <I>lj/charmm/coul/charmm</I> args = inner outer (inner2) (outer2)
@ -35,9 +35,6 @@
<I>lj/charmm/coul/long</I> args = inner outer (cutoff) <I>lj/charmm/coul/long</I> args = inner outer (cutoff)
inner, outer = global switching cutoffs for LJ (and Coulombic if only 2 args) 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) 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> </PRE>
<P><B>Examples:</B> <P><B>Examples:</B>
</P> </P>
@ -52,8 +49,6 @@ pair_coeff * * 100.0 2.0
pair_coeff 1 1 100.0 2.0 150.0 3.5 pair_coeff 1 1 100.0 2.0 150.0 3.5
</PRE> </PRE>
<PRE>pair_style lj/charmm/coul/long 8.0 10.0 <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_style lj/charmm/coul/long 8.0 10.0 9.0
pair_coeff * * 100.0 2.0 pair_coeff * * 100.0 2.0
pair_coeff 1 1 100.0 2.0 150.0 3.5 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 command, then the outer LJ cutoff is used as the single Coulombic
cutoff. cutoff.
</P> </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 <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 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 above, or in the data file or restart files read by the
@ -122,23 +111,25 @@ the pair_style command.
</P> </P>
<HR> <HR>
<P>The styles with an <I>opt</I> suffix are identical to the corresponding <P>Styles with a <I>cuda</I>, <I>gpu</I>, or <I>opt</I> suffix are functionally the same
styles without the suffix, except that it is written in an optimized as the corresponding style without the suffix. They have been
fashion for faster CPU execution. See <A HREF = "doc/Section_accerate.html">this optimized to run faster, depending on your available hardware, as
section</A> of the manual for more details. 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>
<P>The styles with a <I>gpu</I> suffix are identical to the corresponding <P>These accelerated styles are part of the "user-cuda", "gpu", and "opt"
styles without the suffix, except that each processor off-loads its packages respectively. They are only enabled if LAMMPS was built with
pairwise calculations to a GPU. Depending on the hardware available those packages. See the <A HREF = "Section_start.html#2_3">Making LAMMPS</A>
on your system this can provide a speed-up. See <A HREF = "doc/Section_accerate.html">this section for more info.
section</A> of the manual for more details.
</P> </P>
<P>Additional requirements in your input script to run the styles with a <P>You can specify the accelerated styles explicitly in your input script
<I>gpu</I> suffix are as follows: 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>
<P>The <A HREF = "newton.html">newton pair</A> setting must be <I>off</I> and the <A HREF = "fix_gpu.html">fix <P>See <A HREF = "Section_accelerate.html">this section</A> of the manual for more
gpu</A> command must be used. The fix controls the GPU instructions on how to use the accelerated styles effectively.
selection and initialization steps.
</P> </P>
<HR> <HR>
@ -154,10 +145,9 @@ command for details.
<A HREF = "pair_modify.html">pair_modify</A> shift option, since the Lennard-Jones <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. portion of the pair interaction is smoothed to 0.0 at the cutoff.
</P> </P>
<P>The <I>lj/charmm/coul/long</I> and <I>lj/charmm/coul/long/opt</I> pair styles <P>The <I>lj/charmm/coul/long</I> style supports the
support the <A HREF = "pair_modify.html">pair_modify</A> table option since they can <A HREF = "pair_modify.html">pair_modify</A> table option since it can tabulate the
tabulate the short-range portion of the long-range Coulombic short-range portion of the long-range Coulombic interaction.
interaction.
</P> </P>
<P>None of the lj/charmm pair styles support the <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 <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>
<P>The <I>lj/charmm/coul/charmm</I> and <I>lj/charmm/coul/charmm/implicit</I> <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> 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 style is part of the "kspace" package. They are only enabled if
<I>gpu</I> suffix are part of the "opt" or "gpu" packages. They are only LAMMPS was built with those packages. See the <A HREF = "Section_start.html#2_3">Making
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 LAMMPS</A> section for more info. Note that the
molecule and kspace packages are installed by default. molecule and kspace packages are installed by default.
</P> </P>

55
doc/pair_charmm.txt
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@ -16,7 +16,7 @@ pair_style lj/charmm/coul/long/opt command :h3
pair_style style args :pre 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 args = list of arguments for a particular style :ul
{lj/charmm/coul/charmm} args = inner outer (inner2) (outer2) {lj/charmm/coul/charmm} args = inner outer (inner2) (outer2)
inner, outer = global switching cutoffs for Lennard Jones (and Coulombic if only 2 args) 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) inner, outer = global switching cutoffs for LJ (and Coulombic if only 2 args)
inner2, outer2 = global switching cutoffs for Coulombic (optional) inner2, outer2 = global switching cutoffs for Coulombic (optional)
{lj/charmm/coul/long} args = inner outer (cutoff) {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) 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 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_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 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_style lj/charmm/coul/long 8.0 10.0 9.0
pair_coeff * * 100.0 2.0 pair_coeff * * 100.0 2.0
pair_coeff 1 1 100.0 2.0 150.0 3.5 :pre 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 command, then the outer LJ cutoff is used as the single Coulombic
cutoff. 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 The following coefficients must be defined for each pair of atoms
types via the "pair_coeff"_pair_coeff.html command as in the examples 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 above, or in the data file or restart files read by the
@ -114,23 +103,25 @@ the pair_style command.
:line :line
The styles with an {opt} suffix are identical to the corresponding Styles with a {cuda}, {gpu}, or {opt} suffix are functionally the same
styles without the suffix, except that it is written in an optimized as the corresponding style without the suffix. They have been
fashion for faster CPU execution. See "this optimized to run faster, depending on your available hardware, as
section"_doc/Section_accerate.html of the manual for more details. 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 These accelerated styles are part of the "user-cuda", "gpu", and "opt"
styles without the suffix, except that each processor off-loads its packages respectively. They are only enabled if LAMMPS was built with
pairwise calculations to a GPU. Depending on the hardware available those packages. See the "Making LAMMPS"_Section_start.html#2_3
on your system this can provide a speed-up. See "this section for more info.
section"_doc/Section_accerate.html of the manual for more details.
Additional requirements in your input script to run the styles with a You can specify the accelerated styles explicitly in your input script
{gpu} suffix are as follows: 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 See "this section"_Section_accelerate.html of the manual for more
gpu"_fix_gpu.html command must be used. The fix controls the GPU instructions on how to use the accelerated styles effectively.
selection and initialization steps.
:line :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 "pair_modify"_pair_modify.html shift option, since the Lennard-Jones
portion of the pair interaction is smoothed to 0.0 at the cutoff. 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 The {lj/charmm/coul/long} style supports the
support the "pair_modify"_pair_modify.html table option since they can "pair_modify"_pair_modify.html table option since it can tabulate the
tabulate the short-range portion of the long-range Coulombic short-range portion of the long-range Coulombic interaction.
interaction.
None of the lj/charmm pair styles support the None of the lj/charmm pair styles support the
"pair_modify"_pair_modify.html tail option for adding long-range tail "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} The {lj/charmm/coul/charmm} and {lj/charmm/coul/charmm/implicit}
styles are part of the "molecule" package. The {lj/charmm/coul/long} 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 style is part of the "kspace" package. They are only enabled if
{gpu} suffix are part of the "opt" or "gpu" packages. They are only LAMMPS was built with those packages. See the "Making
enabled if LAMMPS was built with those packages. See the "Making
LAMMPS"_Section_start.html#2_3 section for more info. Note that the LAMMPS"_Section_start.html#2_3 section for more info. Note that the
molecule and kspace packages are installed by default. molecule and kspace packages are installed by default.

45
doc/pair_class2.html
View File

@ -23,7 +23,7 @@
</P> </P>
<PRE>pair_style style args <PRE>pair_style style args
</PRE> </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 <LI>args = list of arguments for a particular style
</UL> </UL>
<PRE> <I>lj/class2</I> args = cutoff <PRE> <I>lj/class2</I> args = cutoff
@ -38,7 +38,6 @@
<P><B>Examples:</B> <P><B>Examples:</B>
</P> </P>
<PRE>pair_style lj/class2 10.0 <PRE>pair_style lj/class2 10.0
pair_style lj/class2/gpu 10.0
pair_coeff * * 100.0 2.5 pair_coeff * * 100.0 2.5
pair_coeff 1 2* 100.0 2.5 9.0 pair_coeff 1 2* 100.0 2.5 9.0
</PRE> </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 pair_coeff 1 1 100.0 3.5 9.0 9.0
</PRE> </PRE>
<PRE>pair_style lj/class2/coul/long 10.0 <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_style lj/class2/coul/long 10.0 8.0
pair_coeff * * 100.0 3.0 pair_coeff * * 100.0 3.0
pair_coeff 1 1 100.0 3.5 9.0 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> </CENTER>
<P>Rc is the cutoff. <P>Rc is the cutoff.
</P> </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 <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 Coulombic term as described for the <A HREF = "pair_lj.html">lj/cut</A> pair
styles. styles.
</P> </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>See <A HREF = "#Sun">(Sun)</A> for a description of the COMPASS class2 force field.
</P> </P>
<P>The following coefficients must be defined for each pair of atoms <P>The following coefficients must be defined for each pair of atoms
@ -110,18 +102,25 @@ cutoff distance.
</P> </P>
<HR> <HR>
<P>The styles with a <I>gpu</I> suffix are identical to the corresponding <P>Styles with a <I>cuda</I>, <I>gpu</I>, or <I>opt</I> suffix are functionally the same
styles without the suffix, except that each processor off-loads its as the corresponding style without the suffix. They have been
pairwise calculations to a GPU. Depending on the hardware available optimized to run faster, depending on your available hardware, as
on your system this can provide a speed-up. See <A HREF = "doc/Section_accerate.html">this discussed in <A HREF = "Section_accelerate.html">this section</A> of the manual.
section</A> of the manual for more details. The accelerated styles take the same arguments and should produce the
same results, except for round-off and precision issues.
</P> </P>
<P>Additional requirements in your input script to run the styles with a <P>These accelerated styles are part of the "user-cuda", "gpu", and "opt"
<I>gpu</I> suffix are as follows: 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>
<P>The <A HREF = "newton.html">newton pair</A> setting must be <I>off</I> and the <A HREF = "fix_gpu.html">fix <P>You can specify the accelerated styles explicitly in your input script
gpu</A> command must be used. The fix controls the GPU by including their suffix, or you can use the <A HREF = "Section_start.html#2_6">-suffix command-line
selection and initialization steps. 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>
<P><B>Mixing, shift, table, tail correction, restart, rRESPA info</B>: <P><B>Mixing, shift, table, tail correction, restart, rRESPA info</B>:
</P> </P>
@ -155,11 +154,9 @@ support the <I>inner</I>, <I>middle</I>, <I>outer</I> keywords.
</P> </P>
<P><B>Restrictions:</B> <P><B>Restrictions:</B>
</P> </P>
<P>All of these pair styles, except those ending in "gpu", are part of <P>These styles are part of the "class2" package. They are only enabled
the "class2" package. They are only enabled if LAMMPS was built with if LAMMPS was built with that package. See the <A HREF = "Section_start.html#2_3">Making
that package. The styles with a <I>gpu</I> suffix are part of the "gpu" LAMMPS</A> section for more info.
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>
<P><B>Related commands:</B> <P><B>Related commands:</B>
</P> </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 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 args = list of arguments for a particular style :ul
{lj/class2} args = cutoff {lj/class2} args = cutoff
cutoff = global cutoff for class 2 interactions (distance units) cutoff = global cutoff for class 2 interactions (distance units)
@ -30,7 +30,6 @@ args = list of arguments for a particular style :ul
[Examples:] [Examples:]
pair_style lj/class2 10.0 pair_style lj/class2 10.0
pair_style lj/class2/gpu 10.0
pair_coeff * * 100.0 2.5 pair_coeff * * 100.0 2.5
pair_coeff 1 2* 100.0 2.5 9.0 :pre 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_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 10.0
pair_style lj/class2/coul/long/gpu 10.0
pair_style lj/class2/coul/long 10.0 8.0 pair_style lj/class2/coul/long 10.0 8.0
pair_coeff * * 100.0 3.0 pair_coeff * * 100.0 3.0
pair_coeff 1 1 100.0 3.5 9.0 :pre 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. 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 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 Coulombic term as described for the "lj/cut"_pair_lj.html pair
styles. 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. See "(Sun)"_#Sun for a description of the COMPASS class2 force field.
The following coefficients must be defined for each pair of atoms The following coefficients must be defined for each pair of atoms
@ -102,18 +94,25 @@ cutoff distance.
:line :line
The styles with a {gpu} suffix are identical to the corresponding Styles with a {cuda}, {gpu}, or {opt} suffix are functionally the same
styles without the suffix, except that each processor off-loads its as the corresponding style without the suffix. They have been
pairwise calculations to a GPU. Depending on the hardware available optimized to run faster, depending on your available hardware, as
on your system this can provide a speed-up. See "this discussed in "this section"_Section_accelerate.html of the manual.
section"_doc/Section_accerate.html of the manual for more details. 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 These accelerated styles are part of the "user-cuda", "gpu", and "opt"
{gpu} suffix are as follows: 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 You can specify the accelerated styles explicitly in your input script
gpu"_fix_gpu.html command must be used. The fix controls the GPU by including their suffix, or you can use the "-suffix command-line
selection and initialization steps. 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]: [Mixing, shift, table, tail correction, restart, rRESPA info]:
@ -147,11 +146,9 @@ support the {inner}, {middle}, {outer} keywords.
[Restrictions:] [Restrictions:]
All of these pair styles, except those ending in "gpu", are part of These styles are part of the "class2" package. They are only enabled
the "class2" package. They are only enabled if LAMMPS was built with if LAMMPS was built with that package. See the "Making
that package. The styles with a {gpu} suffix are part of the "gpu" LAMMPS"_Section_start.html#2_3 section for more info.
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:] [Related commands:]

49
doc/pair_cmm.html
View File

@ -23,13 +23,11 @@
</P> </P>
<PRE>pair_style style args <PRE>pair_style style args
</PRE> </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 <LI>args = list of arguments for a particular style
</UL> </UL>
<PRE> <I>cg/cmm</I> args = cutoff <PRE> <I>cg/cmm</I> args = cutoff
cutoff = global cutoff for Lennard Jones interactions (distance units) 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) <I>cg/cmm/coul/cut</I> args = cutoff (cutoff2) (kappa)
cutoff = global cutoff for LJ (and Coulombic if only 1 arg) (distance units) cutoff = global cutoff for LJ (and Coulombic if only 1 arg) (distance units)
cutoff2 = global cutoff for Coulombic (optional) (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) cutoff = global cutoff for LJ (and Coulombic if only 1 arg) (distance units)
cutoff2 = global cutoff for Coulombic (optional) (distance units) cutoff2 = global cutoff for Coulombic (optional) (distance units)
</PRE> </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><B>Examples:</B>
</P> </P>
<PRE>pair_style cg/cmm 2.5 <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 <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. <A HREF = "#Shinoda">(Shinoda)</A> and <A HREF = "#DeVane">(DeVane)</A>. Rc is the cutoff.
</P> </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>Style <I>cg/cmm/coul/cut</I> adds a Coulombic pairwise interaction given by
</P> </P>
<CENTER><IMG SRC = "Eqs/pair_coulomb.jpg"> <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; pairwise interactions within this distance are computed directly;
interactions outside that distance are computed in reciprocal space. interactions outside that distance are computed in reciprocal space.
</P> </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 <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 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 above, or in the data file or restart files read by the
@ -129,18 +117,25 @@ pair_style command.
</P> </P>
<HR> <HR>
<P>The styles with a <I>gpu</I> suffix are identical to the corresponding <P>Styles with a <I>cuda</I>, <I>gpu</I>, or <I>opt</I> suffix are functionally the same
styles without the suffix, except that each processor off-loads its as the corresponding style without the suffix. They have been
pairwise calculations to a GPU. Depending on the hardware available optimized to run faster, depending on your available hardware, as
on your system this can provide a speed-up. See <A HREF = "doc/Section_accerate.html">this discussed in <A HREF = "Section_accelerate.html">this section</A> of the manual.
section</A> of the manual for more details. The accelerated styles take the same arguments and should produce the
same results, except for round-off and precision issues.
</P> </P>
<P>Additional requirements in your input script to run the styles with a <P>These accelerated styles are part of the "user-cuda", "gpu", and "opt"
<I>gpu</I> suffix are as follows: 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>
<P>The <A HREF = "newton.html">newton pair</A> setting must be <I>off</I> and the <A HREF = "fix_gpu.html">fix <P>You can specify the accelerated styles explicitly in your input script
gpu</A> command must be used. The fix controls the GPU by including their suffix, or you can use the <A HREF = "Section_start.html#2_6">-suffix command-line
selection and initialization steps. 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>
<HR> <HR>
@ -175,12 +170,10 @@ See the <A HREF = "run_style.html">run_style</A> command for details.
<P><B>Restrictions:</B> <P><B>Restrictions:</B>
</P> </P>
<P>All of the cg/cmm pair styles are part of the "user-cg-cmm" <P>All of the cg/cmm pair styles are part of the "user-cg-cmm" package.
package. They are only enabled if LAMMPS was built with that package.
The <I>cg/cmm/coul/long</I> style also requires the "kspace" package to be 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 built (which is enabled by default). They are only enabled if LAMMPS
are part of the "gpu" package. They are only enabled if LAMMPS was was built with that package. See the <A HREF = "Section_start.html#2_3">Making
built with that package. See the <A HREF = "Section_start.html#2_3">Making
LAMMPS</A> section for more info. LAMMPS</A> section for more info.
</P> </P>
<P><B>Related commands:</B> <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 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 args = list of arguments for a particular style :ul
{cg/cmm} args = cutoff {cg/cmm} args = cutoff
cutoff = global cutoff for Lennard Jones interactions (distance units) 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) {cg/cmm/coul/cut} args = cutoff (cutoff2) (kappa)
cutoff = global cutoff for LJ (and Coulombic if only 1 arg) (distance units) cutoff = global cutoff for LJ (and Coulombic if only 1 arg) (distance units)
cutoff2 = global cutoff for Coulombic (optional) (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) {cg/cmm/coul/long} args = cutoff (cutoff2)
cutoff = global cutoff for LJ (and Coulombic if only 1 arg) (distance units) cutoff = global cutoff for LJ (and Coulombic if only 1 arg) (distance units)
cutoff2 = global cutoff for Coulombic (optional) (distance units) :pre 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:] [Examples:]
@ -56,9 +51,6 @@ given by
as required for the CMM Coarse-grained MD parametrization discussed in as required for the CMM Coarse-grained MD parametrization discussed in
"(Shinoda)"_#Shinoda and "(DeVane)"_#DeVane. Rc is the cutoff. "(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 Style {cg/cmm/coul/cut} adds a Coulombic pairwise interaction given by
:c,image(Eqs/pair_coulomb.jpg) :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; pairwise interactions within this distance are computed directly;
interactions outside that distance are computed in reciprocal space. 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 The following coefficients must be defined for each pair of atoms
types via the "pair_coeff"_pair_coeff.html command as in the examples 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 above, or in the data file or restart files read by the
@ -120,18 +109,25 @@ pair_style command.
:line :line
The styles with a {gpu} suffix are identical to the corresponding Styles with a {cuda}, {gpu}, or {opt} suffix are functionally the same
styles without the suffix, except that each processor off-loads its as the corresponding style without the suffix. They have been
pairwise calculations to a GPU. Depending on the hardware available optimized to run faster, depending on your available hardware, as
on your system this can provide a speed-up. See "this discussed in "this section"_Section_accelerate.html of the manual.
section"_doc/Section_accerate.html of the manual for more details. 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 These accelerated styles are part of the "user-cuda", "gpu", and "opt"
{gpu} suffix are as follows: 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 You can specify the accelerated styles explicitly in your input script
gpu"_fix_gpu.html command must be used. The fix controls the GPU by including their suffix, or you can use the "-suffix command-line
selection and initialization steps. 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 :line
@ -166,12 +162,10 @@ See the "run_style"_run_style.html command for details.
[Restrictions:] [Restrictions:]
All of the cg/cmm pair styles are part of the "user-cg-cmm" All of the cg/cmm pair styles are part of the "user-cg-cmm" package.
package. They are only enabled if LAMMPS was built with that package.
The {cg/cmm/coul/long} style also requires the "kspace" package to be 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 built (which is enabled by default). They are only enabled if LAMMPS
are part of the "gpu" package. They are only enabled if LAMMPS was was built with that package. See the "Making
built with that package. See the "Making
LAMMPS"_Section_start.html#2_3 section for more info. LAMMPS"_Section_start.html#2_3 section for more info.
[Related commands:] [Related commands:]

45
doc/pair_eam.html
View File

@ -27,24 +27,21 @@
</P> </P>
<PRE>pair_style style <PRE>pair_style style
</PRE> </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> </UL>
<P><B>Examples:</B> <P><B>Examples:</B>
</P> </P>
<PRE>pair_style eam <PRE>pair_style eam
pair_style eam/opt
pair_coeff * * cuu3 pair_coeff * * cuu3
pair_coeff 1*3 1*3 niu3.eam pair_coeff 1*3 1*3 niu3.eam
</PRE> </PRE>
<PRE>pair_style eam/alloy <PRE>pair_style eam/alloy
pair_style eam/alloy/opt
pair_coeff * * ../potentials/NiAlH_jea.eam.alloy Ni Al Ni Ni pair_coeff * * ../potentials/NiAlH_jea.eam.alloy Ni Al Ni Ni
</PRE> </PRE>
<PRE>pair_style eam/cd <PRE>pair_style eam/cd
pair_coeff * * ../potentials/FeCr.cdeam Fe Cr pair_coeff * * ../potentials/FeCr.cdeam Fe Cr
</PRE> </PRE>
<PRE>pair_style eam/fs <PRE>pair_style eam/fs
pair_style eam/fs/opt
pair_coeff * * NiAlH_jea.eam.fs Ni Al Ni Ni pair_coeff * * NiAlH_jea.eam.fs Ni Al Ni Ni
</PRE> </PRE>
<P><B>Description:</B> <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 Both summations in the formula are over all neighbors J of atom I
within the cutoff distance. within the cutoff distance.
</P> </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, <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 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 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 interactions. Thus they allow more generality than <I>funcfl</I> files for
modeling alloys. modeling alloys.
</P> </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 <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 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 (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 electron density at an atomic site depending on the identity of the
element at that atomic site. element at that atomic site.
</P> </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> <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 reads a DYNAMO <I>setfl</I> file that has been extended to include
additional rho_alpha_beta arrays of tabulated values. A discussion of additional rho_alpha_beta arrays of tabulated values. A discussion of
@ -371,10 +359,25 @@ are listed.
</P> </P>
<HR> <HR>
<P>The styles with an <I>opt</I> suffix are identical to the corresponding <P>Styles with a <I>cuda</I>, <I>gpu</I>, or <I>opt</I> suffix are functionally the same
styles without the suffix, except that it is written in an optimized as the corresponding style without the suffix. They have been
fashion for faster CPU execution. See <A HREF = "doc/Section_accerate.html">this optimized to run faster, depending on your available hardware, as
section</A> of the manual for more details. 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> </P>
<HR> <HR>
@ -401,11 +404,9 @@ an input script that reads a restart file.
<P><B>Restrictions:</B> <P><B>Restrictions:</B>
</P> </P>
<P>All of these styles except those ending in <I>opt</I> and the <I>eam/cd</I> <P>All of these styles except the <I>eam/cd</I> style are part of the
style are part of the "manybody" package. They are only enabled if "manybody" package. They are only enabled if LAMMPS was built with
LAMMPS was built with that package (which it is by default). The that package (which it is by default). See the <A HREF = "Section_start.html#2_3">Making
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
LAMMPS</A> section for more info. LAMMPS</A> section for more info.
</P> </P>
<P>The <I>eam/cd</I> style is part of the "user-cd-eam" package and also <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 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:] [Examples:]
pair_style eam pair_style eam
pair_style eam/opt
pair_coeff * * cuu3 pair_coeff * * cuu3
pair_coeff 1*3 1*3 niu3.eam :pre pair_coeff 1*3 1*3 niu3.eam :pre
pair_style eam/alloy pair_style eam/alloy
pair_style eam/alloy/opt
pair_coeff * * ../potentials/NiAlH_jea.eam.alloy Ni Al Ni Ni :pre pair_coeff * * ../potentials/NiAlH_jea.eam.alloy Ni Al Ni Ni :pre
pair_style eam/cd pair_style eam/cd
pair_coeff * * ../potentials/FeCr.cdeam Fe Cr :pre pair_coeff * * ../potentials/FeCr.cdeam Fe Cr :pre
pair_style eam/fs pair_style eam/fs
pair_style eam/fs/opt
pair_coeff * * NiAlH_jea.eam.fs Ni Al Ni Ni :pre pair_coeff * * NiAlH_jea.eam.fs Ni Al Ni Ni :pre
[Description:] [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 Both summations in the formula are over all neighbors J of atom I
within the cutoff distance. 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, 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 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 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 interactions. Thus they allow more generality than {funcfl} files for
modeling alloys. 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 For style {eam/alloy}, potential values are read from a file that is
in the DYNAMO multi-element {setfl} format, except that element names 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 (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 electron density at an atomic site depending on the identity of the
element at that atomic site. 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} The associated "pair_coeff"_pair_coeff.html command for style {eam/fs}
reads a DYNAMO {setfl} file that has been extended to include reads a DYNAMO {setfl} file that has been extended to include
additional rho_alpha_beta arrays of tabulated values. A discussion of additional rho_alpha_beta arrays of tabulated values. A discussion of
@ -362,10 +350,25 @@ are listed.
:line :line
The styles with an {opt} suffix are identical to the corresponding Styles with a {cuda}, {gpu}, or {opt} suffix are functionally the same
styles without the suffix, except that it is written in an optimized as the corresponding style without the suffix. They have been
fashion for faster CPU execution. See "this optimized to run faster, depending on your available hardware, as
section"_doc/Section_accerate.html of the manual for more details. 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 :line
@ -392,11 +395,9 @@ The eam pair styles can only be used via the {pair} keyword of the
[Restrictions:] [Restrictions:]
All of these styles except those ending in {opt} and the {eam/cd} All of these styles except the {eam/cd} style are part of the
style are part of the "manybody" package. They are only enabled if "manybody" package. They are only enabled if LAMMPS was built with
LAMMPS was built with that package (which it is by default). The that package (which it is by default). See the "Making
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
LAMMPS"_Section_start.html#2_3 section for more info. LAMMPS"_Section_start.html#2_3 section for more info.
The {eam/cd} style is part of the "user-cd-eam" package and also 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> </P>
<PRE>pair_style gayberne gamma upsilon mu cutoff <PRE>pair_style gayberne gamma upsilon mu cutoff
</PRE> </PRE>
<PRE>pair_style gayberne/gpu gamma upsilon mu cutoff <UL><LI>gamma = shift for potential minimum (typically 1)
</PRE>
<UL><LI>style = <I>gayberne</I> or <I>gayberne/gpu</I>
<LI>gamma = shift for potential minimum (typically 1)
<LI>upsilon = exponent for eta orientation-dependent energy function <LI>upsilon = exponent for eta orientation-dependent energy function
<LI>mu = exponent for chi orientation-dependent energy function <LI>mu = exponent for chi orientation-dependent energy function
<LI>cutoff = global cutoff for interactions (distance units) <LI>cutoff = global cutoff for interactions (distance units)
@ -28,7 +25,6 @@
<P><B>Examples:</B> <P><B>Examples:</B>
</P> </P>
<PRE>pair_style gayberne 1.0 1.0 1.0 10.0 <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 pair_coeff * * 1.0 1.7 1.7 3.4 3.4 1.0 1.0 1.0
</PRE> </PRE>
<P><B>Description:</B> <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 Lennard-Jones interaction (see details below for when Gay-Berne treats
a particle as "spherical"). a particle as "spherical").
</P> </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 <P>For large uniform molecules it has been shown that the energy
parameters are approximately representable in terms of local contact parameters are approximately representable in terms of local contact
curvatures <A HREF = "#Everaers">(Everaers)</A>: curvatures <A HREF = "#Everaers">(Everaers)</A>:
@ -139,18 +132,25 @@ pair_coeff sigma to 1.0 as well.
</P> </P>
<HR> <HR>
<P>The styles with a <I>gpu</I> suffix are identical to the corresponding <P>Styles with a <I>cuda</I>, <I>gpu</I>, or <I>opt</I> suffix are functionally the same
styles without the suffix, except that each processor off-loads its as the corresponding style without the suffix. They have been
pairwise calculations to a GPU. Depending on the hardware available optimized to run faster, depending on your available hardware, as
on your system this can provide a speed-up. See <A HREF = "doc/Section_accerate.html">this discussed in <A HREF = "Section_accelerate.html">this section</A> of the manual.
section</A> of the manual for more details. The accelerated styles take the same arguments and should produce the
same results, except for round-off and precision issues.
</P> </P>
<P>Additional requirements in your input script to run the styles with a <P>These accelerated styles are part of the "user-cuda", "gpu", and "opt"
<I>gpu</I> suffix are as follows: 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>
<P>The <A HREF = "newton.html">newton pair</A> setting must be <I>off</I> and the <A HREF = "fix_gpu.html">fix <P>You can specify the accelerated styles explicitly in your input script
gpu</A> command must be used. The fix controls the GPU by including their suffix, or you can use the <A HREF = "Section_start.html#2_6">-suffix command-line
selection and initialization steps. 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>
<HR> <HR>
@ -185,9 +185,8 @@ to be specified in an input script that reads a restart file.
<P><B>Restrictions:</B> <P><B>Restrictions:</B>
</P> </P>
<P>The <I>gayberne</I> style is part of the "asphere" package. The styles <P>The <I>gayberne</I> style is part of the "asphere" package. It is only
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
enabled if LAMMPS was built with those packages. See the <A HREF = "Section_start.html#2_3">Making
LAMMPS</A> section for more info. LAMMPS</A> section for more info.
</P> </P>
<P>These pair style require that atoms store torque and a quaternion to <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:] [Syntax:]
pair_style gayberne gamma upsilon mu cutoff :pre 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) gamma = shift for potential minimum (typically 1)
upsilon = exponent for eta orientation-dependent energy function upsilon = exponent for eta orientation-dependent energy function
mu = exponent for chi 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:] [Examples:]
pair_style gayberne 1.0 1.0 1.0 10.0 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 pair_coeff * * 1.0 1.7 1.7 3.4 3.4 1.0 1.0 1.0 :pre
[Description:] [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 Lennard-Jones interaction (see details below for when Gay-Berne treats
a particle as "spherical"). 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 For large uniform molecules it has been shown that the energy
parameters are approximately representable in terms of local contact parameters are approximately representable in terms of local contact
curvatures "(Everaers)"_#Everaers: curvatures "(Everaers)"_#Everaers:
@ -134,18 +128,25 @@ pair_coeff sigma to 1.0 as well.
:line :line
The styles with a {gpu} suffix are identical to the corresponding Styles with a {cuda}, {gpu}, or {opt} suffix are functionally the same
styles without the suffix, except that each processor off-loads its as the corresponding style without the suffix. They have been
pairwise calculations to a GPU. Depending on the hardware available optimized to run faster, depending on your available hardware, as
on your system this can provide a speed-up. See "this discussed in "this section"_Section_accelerate.html of the manual.
section"_doc/Section_accerate.html of the manual for more details. 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 These accelerated styles are part of the "user-cuda", "gpu", and "opt"
{gpu} suffix are as follows: 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 You can specify the accelerated styles explicitly in your input script
gpu"_fix_gpu.html command must be used. The fix controls the GPU by including their suffix, or you can use the "-suffix command-line
selection and initialization steps. 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 :line
@ -180,9 +181,8 @@ This pair style can only be used via the {pair} keyword of the
[Restrictions:] [Restrictions:]
The {gayberne} style is part of the "asphere" package. The styles The {gayberne} style is part of the "asphere" package. It is only
with a {gpu} suffix are part of the "gpu" package. They are only enabled if LAMMPS was built with that package. See the "Making
enabled if LAMMPS was built with those packages. See the "Making
LAMMPS"_Section_start.html#2_3 section for more info. LAMMPS"_Section_start.html#2_3 section for more info.
These pair style require that atoms store torque and a quaternion to These pair style require that atoms store torque and a quaternion to

67
doc/pair_lj.html
View File

@ -31,21 +31,14 @@
</P> </P>
<PRE>pair_style style args <PRE>pair_style style args
</PRE> </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 <LI>args = list of arguments for a particular style
</UL> </UL>
<PRE> <I>lj/cut</I> args = cutoff <PRE> <I>lj/cut</I> args = cutoff
cutoff = global cutoff for Lennard Jones interactions (distance units) 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) <I>lj/cut/coul/cut</I> args = cutoff (cutoff2)
cutoff = global cutoff for LJ (and Coulombic if only 1 arg) (distance units) cutoff = global cutoff for LJ (and Coulombic if only 1 arg) (distance units)
cutoff2 = global cutoff for Coulombic (optional) (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) <I>lj/cut/coul/debye</I> args = kappa cutoff (cutoff2)
kappa = Debye length (inverse distance units) kappa = Debye length (inverse distance units)
cutoff = global cutoff for LJ (and Coulombic if only 1 arg) (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) <I>lj/cut/coul/long</I> args = cutoff (cutoff2)
cutoff = global cutoff for LJ (and Coulombic if only 1 arg) (distance units) cutoff = global cutoff for LJ (and Coulombic if only 1 arg) (distance units)
cutoff2 = global cutoff for Coulombic (optional) (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) <I>lj/cut/coul/long/tip4p</I> args = otype htype btype atype qdist cutoff (cutoff2)
otype,htype = atom types for TIP4P O and H otype,htype = atom types for TIP4P O and H
btype,atype = bond and angle types for TIP4P waters btype,atype = bond and angle types for TIP4P waters
@ -66,13 +56,10 @@
<P><B>Examples:</B> <P><B>Examples:</B>
</P> </P>
<PRE>pair_style lj/cut 2.5 <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
pair_coeff 1 1 1 1.1 2.8 pair_coeff 1 1 1 1.1 2.8
</PRE> </PRE>
<PRE>pair_style lj/cut/coul/cut 10.0 <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_style lj/cut/coul/cut 10.0 8.0
pair_coeff * * 100.0 3.0 pair_coeff * * 100.0 3.0
pair_coeff 1 1 100.0 3.5 9.0 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 pair_coeff 1 1 1.0 1.5 2.5 5.0
</PRE> </PRE>
<PRE>pair_style lj/cut/coul/long 10.0 <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_style lj/cut/coul/long 10.0 8.0
pair_coeff * * 100.0 3.0 pair_coeff * * 100.0 3.0
pair_coeff 1 1 100.0 3.5 9.0 pair_coeff 1 1 100.0 3.5 9.0
@ -104,12 +90,6 @@ given by
</CENTER> </CENTER>
<P>Rc is the cutoff. <P>Rc is the cutoff.
</P> </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>Style <I>lj/cut/coul/cut</I> adds a Coulombic pairwise interaction given by
</P> </P>
<CENTER><IMG SRC = "Eqs/pair_coulomb.jpg"> <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 Coulombic terms. If two cutoffs are specified, they are used as
cutoffs for the LJ and Coulombic terms respectively. cutoffs for the LJ and Coulombic terms respectively.
</P> </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 <P>Style <I>lj/cut/coul/debye</I> adds an additional exp() damping factor
to the Coulombic term, given by to the Coulombic term, given by
</P> </P>
@ -140,9 +117,6 @@ option. The Coulombic cutoff specified for this style means that
pairwise interactions within this distance are computed directly; pairwise interactions within this distance are computed directly;
interactions outside that distance are computed in reciprocal space. interactions outside that distance are computed in reciprocal space.
</P> </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 <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 <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 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> </P>
<HR> <HR>
<P>The styles with an <I>opt</I> suffix are identical to the corresponding <P>Styles with a <I>cuda</I>, <I>gpu</I>, or <I>opt</I> suffix are functionally the same
styles without the suffix, except that it is written in an optimized as the corresponding style without the suffix. They have been
fashion for faster CPU execution. See <A HREF = "doc/Section_accerate.html">this optimized to run faster, depending on your available hardware, as
section</A> of the manual for more details. 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>
<P>The styles with a <I>gpu</I> suffix are identical to the corresponding <P>These accelerated styles are part of the "user-cuda", "gpu", and "opt"
styles without the suffix, except that each processor off-loads its packages respectively. They are only enabled if LAMMPS was built with
pairwise calculations to a GPU. Depending on the hardware available those packages. See the <A HREF = "Section_start.html#2_3">Making LAMMPS</A>
on your system this can provide a speed-up. See <A HREF = "doc/Section_accerate.html">this section for more info.
section</A> of the manual for more details.
</P> </P>
<P>Additional requirements in your input script to run the styles with a <P>You can specify the accelerated styles explicitly in your input script
<I>gpu</I> suffix are as follows: 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>
<P>The <A HREF = "newton.html">newton pair</A> setting must be <I>off</I> and the <A HREF = "fix_gpu.html">fix <P>See <A HREF = "Section_accelerate.html">this section</A> of the manual for more
gpu</A> command must be used. The fix controls the GPU instructions on how to use the accelerated styles effectively.
selection and initialization steps.
</P> </P>
<HR> <HR>
@ -246,11 +222,10 @@ See the <A HREF = "run_style.html">run_style</A> command for details.
<P><B>Restrictions:</B> <P><B>Restrictions:</B>
</P> </P>
<P>The <I>lj/cut/coul/long</I> and <I>lj/cut/coul/long/tip4p</I> styles are part of <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 the "kspace" package. They are only enabled if LAMMPS was built with
part of the "opt" or "gpu" packages. They are only enabled if LAMMPS those packages. See the <A HREF = "Section_start.html#2_3">Making LAMMPS</A>
was built with those packages. See the <A HREF = "Section_start.html#2_3">Making section for more info. Note that the kspace package is installed by
LAMMPS</A> section for more info. Note that the default.
kspace package is installed by default.
</P> </P>
<P><B>Related commands:</B> <P><B>Related commands:</B>
</P> </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 pair_style style args :pre
style = {lj/cut} or {lj/cut/gpu} or {lj/cut/opt} or {lj/cut/coul/cut} \ style = {lj/cut} or {lj/cut/coul/cut} or {lj/cut/coul/debye} or {lj/cut/coul/long} or {lj/cut/coul/long/tip4p}
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 args = list of arguments for a particular style :ul
{lj/cut} args = cutoff {lj/cut} args = cutoff
cutoff = global cutoff for Lennard Jones interactions (distance units) 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) {lj/cut/coul/cut} args = cutoff (cutoff2)
cutoff = global cutoff for LJ (and Coulombic if only 1 arg) (distance units) cutoff = global cutoff for LJ (and Coulombic if only 1 arg) (distance units)
cutoff2 = global cutoff for Coulombic (optional) (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) {lj/cut/coul/debye} args = kappa cutoff (cutoff2)
kappa = Debye length (inverse distance units) kappa = Debye length (inverse distance units)
cutoff = global cutoff for LJ (and Coulombic if only 1 arg) (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) {lj/cut/coul/long} args = cutoff (cutoff2)
cutoff = global cutoff for LJ (and Coulombic if only 1 arg) (distance units) cutoff = global cutoff for LJ (and Coulombic if only 1 arg) (distance units)
cutoff2 = global cutoff for Coulombic (optional) (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) {lj/cut/coul/long/tip4p} args = otype htype btype atype qdist cutoff (cutoff2)
otype,htype = atom types for TIP4P O and H otype,htype = atom types for TIP4P O and H
btype,atype = bond and angle types for TIP4P waters btype,atype = bond and angle types for TIP4P waters
@ -55,13 +44,10 @@ args = list of arguments for a particular style :ul
[Examples:] [Examples:]
pair_style lj/cut 2.5 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
pair_coeff 1 1 1 1.1 2.8 :pre pair_coeff 1 1 1 1.1 2.8 :pre
pair_style lj/cut/coul/cut 10.0 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_style lj/cut/coul/cut 10.0 8.0
pair_coeff * * 100.0 3.0 pair_coeff * * 100.0 3.0
pair_coeff 1 1 100.0 3.5 9.0 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_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 10.0
pair_style lj/cut/coul/long/gpu 10.0
pair_style lj/cut/coul/long 10.0 8.0 pair_style lj/cut/coul/long 10.0 8.0
pair_coeff * * 100.0 3.0 pair_coeff * * 100.0 3.0
pair_coeff 1 1 100.0 3.5 9.0 :pre pair_coeff 1 1 100.0 3.5 9.0 :pre
@ -93,12 +78,6 @@ given by
Rc is the cutoff. 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 Style {lj/cut/coul/cut} adds a Coulombic pairwise interaction given by
:c,image(Eqs/pair_coulomb.jpg) :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 Coulombic terms. If two cutoffs are specified, they are used as
cutoffs for the LJ and Coulombic terms respectively. 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 Style {lj/cut/coul/debye} adds an additional exp() damping factor
to the Coulombic term, given by 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; pairwise interactions within this distance are computed directly;
interactions outside that distance are computed in reciprocal space. 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 Style {lj/cut/coul/long/tip4p} implements the TIP4P water model of
"(Jorgensen)"_#Jorgensen, which introduces a massless site located a "(Jorgensen)"_#Jorgensen, which introduces a massless site located a
short distance away from the oxygen atom along the bisector of the HOH 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 :line
The styles with an {opt} suffix are identical to the corresponding Styles with a {cuda}, {gpu}, or {opt} suffix are functionally the same
styles without the suffix, except that it is written in an optimized as the corresponding style without the suffix. They have been
fashion for faster CPU execution. See "this optimized to run faster, depending on your available hardware, as
section"_doc/Section_accerate.html of the manual for more details. 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 These accelerated styles are part of the "user-cuda", "gpu", and "opt"
styles without the suffix, except that each processor off-loads its packages respectively. They are only enabled if LAMMPS was built with
pairwise calculations to a GPU. Depending on the hardware available those packages. See the "Making LAMMPS"_Section_start.html#2_3
on your system this can provide a speed-up. See "this section for more info.
section"_doc/Section_accerate.html of the manual for more details.
Additional requirements in your input script to run the styles with a You can specify the accelerated styles explicitly in your input script
{gpu} suffix are as follows: 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 See "this section"_Section_accelerate.html of the manual for more
gpu"_fix_gpu.html command must be used. The fix controls the GPU instructions on how to use the accelerated styles effectively.
selection and initialization steps.
:line :line
@ -235,11 +210,10 @@ See the "run_style"_run_style.html command for details.
[Restrictions:] [Restrictions:]
The {lj/cut/coul/long} and {lj/cut/coul/long/tip4p} styles are part of 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 the "kspace" package. They are only enabled if LAMMPS was built with
part of the "opt" or "gpu" packages. They are only enabled if LAMMPS those packages. See the "Making LAMMPS"_Section_start.html#2_3
was built with those packages. See the "Making section for more info. Note that the kspace package is installed by
LAMMPS"_Section_start.html#2_3 section for more info. Note that the default.
kspace package is installed by default.
[Related commands:] [Related commands:]

42
doc/pair_lj96_cut.html
View File

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

40
doc/pair_lj96_cut.txt
View File

@ -11,15 +11,13 @@ pair_style lj96/cut/gpu command :h3
[Syntax:] [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 cutoff = global cutoff for lj96/cut interactions (distance units) :ul
[Examples:] [Examples:]
pair_style lj96/cut 2.5 pair_style lj96/cut 2.5
pair_style lj96/cut/gpu 2.5
pair_coeff * * 1.0 1.0 4.0 pair_coeff * * 1.0 1.0 4.0
pair_coeff 1 1 1.0 1.0 :pre 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. 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 The following coefficients must be defined for each pair of atoms
types via the "pair_coeff"_pair_coeff.html command as in the examples 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 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 :line
The styles with a {gpu} suffix are identical to the corresponding Styles with a {cuda}, {gpu}, or {opt} suffix are functionally the same
styles without the suffix, except that each processor off-loads its as the corresponding style without the suffix. They have been
pairwise calculations to a GPU. Depending on the hardware available optimized to run faster, depending on your available hardware, as
on your system this can provide a speed-up. See "this discussed in "this section"_Section_accelerate.html of the manual.
section"_doc/Section_accerate.html of the manual for more details. 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 These accelerated styles are part of the "user-cuda", "gpu", and "opt"
{gpu} suffix are as follows: 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 You can specify the accelerated styles explicitly in your input script
gpu"_fix_gpu.html command must be used. The fix controls the GPU by including their suffix, or you can use the "-suffix command-line
selection and initialization steps. 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 :line
@ -94,11 +96,7 @@ details.
:line :line
[Restrictions:] [Restrictions:] none
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.
[Related commands:] [Related commands:]

38
doc/pair_lj_expand.html
View File

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

37
doc/pair_lj_expand.txt
View File

@ -12,7 +12,6 @@ pair_style lj/expand/gpu command :h3
[Syntax:] [Syntax:]
pair_style lj/expand cutoff :pre pair_style lj/expand cutoff :pre
pair_style lj/expand/gpu cutoff :pre
cutoff = global cutoff for lj/expand interactions (distance units) :ul 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 The delta values can be positive or negative. The last coefficient is
optional. If not specified, the global LJ cutoff is used. 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 :line
The styles with a {gpu} suffix are identical to the corresponding Styles with a {cuda}, {gpu}, or {opt} suffix are functionally the same
styles without the suffix, except that each processor off-loads its as the corresponding style without the suffix. They have been
pairwise calculations to a GPU. Depending on the hardware available optimized to run faster, depending on your available hardware, as
on your system this can provide a speed-up. See "this discussed in "this section"_Section_accelerate.html of the manual.
section"_doc/Section_accerate.html of the manual for more details. 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 These accelerated styles are part of the "user-cuda", "gpu", and "opt"
{gpu} suffix are as follows: 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 You can specify the accelerated styles explicitly in your input script
gpu"_fix_gpu.html command must be used. The fix controls the GPU by including their suffix, or you can use the "-suffix command-line
selection and initialization steps. 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 :line
@ -97,11 +100,7 @@ This pair style can only be used via the {pair} keyword of the
:line :line
[Restrictions:] [Restrictions:] none
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.
[Related commands:] [Related commands:]

48
doc/pair_morse.html
View File

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

46
doc/pair_morse.txt
View File

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

41
doc/pair_resquared.html
View File

@ -15,15 +15,13 @@
</H3> </H3>
<P><B>Syntax:</B> <P><B>Syntax:</B>
</P> </P>
<PRE>pair_style style cutoff <PRE>pair_style resquared cutoff
</PRE> </PRE>
<UL><LI>style = <I>resquared</I> or <I>resquared/gpu</I> <UL><LI>cutoff = global cutoff for interactions (distance units)
<LI>cutoff = global cutoff for interactions (distance units)
</UL> </UL>
<P><B>Examples:</B> <P><B>Examples:</B>
</P> </P>
<PRE>pair_style resquared 10.0 <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 pair_coeff * * 1.0 1.0 1.7 3.4 3.4 1.0 1.0 1.0
</PRE> </PRE>
<P><B>Description:</B> <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 size sigma. The distinction is made to allow the pair style to make
efficient calculations of ellipsoid/solvent interactions. efficient calculations of ellipsoid/solvent interactions.
</P> </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 <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>. in <A HREF = "PDF/pair_resquared_extra.pdf">this supplementary document</A>.
</P> </P>
@ -150,18 +145,25 @@ specified in the pair_style command is used.
</P> </P>
<HR> <HR>
<P>The styles with a <I>gpu</I> suffix are identical to the corresponding <P>Styles with a <I>cuda</I>, <I>gpu</I>, or <I>opt</I> suffix are functionally the same
styles without the suffix, except that each processor off-loads its as the corresponding style without the suffix. They have been
pairwise calculations to a GPU. Depending on the hardware available optimized to run faster, depending on your available hardware, as
on your system this can provide a speed-up. See <A HREF = "doc/Section_accerate.html">this discussed in <A HREF = "Section_accelerate.html">this section</A> of the manual.
section</A> of the manual for more details. The accelerated styles take the same arguments and should produce the
same results, except for round-off and precision issues.
</P> </P>
<P>Additional requirements in your input script to run the styles with a <P>These accelerated styles are part of the "user-cuda", "gpu", and "opt"
<I>gpu</I> suffix are as follows: 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>
<P>The <A HREF = "newton.html">newton pair</A> setting must be <I>off</I> and the <A HREF = "fix_gpu.html">fix <P>You can specify the accelerated styles explicitly in your input script
gpu</A> command must be used. The fix controls the GPU by including their suffix, or you can use the <A HREF = "Section_start.html#2_6">-suffix command-line
selection and initialization steps. 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>
<HR> <HR>
@ -203,9 +205,8 @@ command</A>.
<P><B>Restrictions:</B> <P><B>Restrictions:</B>
</P> </P>
<P>This style is part of the "asphere" package. The styles with a <I>gpu</I> <P>This style is part of the "asphere" package. It is only enabled if
suffix are part of the "gpu" package. They are only enabled if LAMMPS LAMMPS was built with that package. See the <A HREF = "Section_start.html#2_3">Making
was built with those packages. See the <A HREF = "Section_start.html#2_3">Making
LAMMPS</A> section for more info. LAMMPS</A> section for more info.
</P> </P>
<P>This pair style requires that atoms be ellipsoids as defined by the <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:] [Syntax:]
pair_style style cutoff :pre pair_style resquared cutoff :pre
style = {resquared} or {resquared/gpu}
cutoff = global cutoff for interactions (distance units) :ul cutoff = global cutoff for interactions (distance units) :ul
[Examples:] [Examples:]
pair_style resquared 10.0 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 pair_coeff * * 1.0 1.0 1.7 3.4 3.4 1.0 1.0 1.0 :pre
[Description:] [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 size sigma. The distinction is made to allow the pair style to make
efficient calculations of ellipsoid/solvent interactions. 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 Details for the equations used are given in the references below and
in "this supplementary document"_PDF/pair_resquared_extra.pdf. in "this supplementary document"_PDF/pair_resquared_extra.pdf.
@ -146,18 +141,25 @@ specified in the pair_style command is used.
:line :line
The styles with a {gpu} suffix are identical to the corresponding Styles with a {cuda}, {gpu}, or {opt} suffix are functionally the same
styles without the suffix, except that each processor off-loads its as the corresponding style without the suffix. They have been
pairwise calculations to a GPU. Depending on the hardware available optimized to run faster, depending on your available hardware, as
on your system this can provide a speed-up. See "this discussed in "this section"_Section_accelerate.html of the manual.
section"_doc/Section_accerate.html of the manual for more details. 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 These accelerated styles are part of the "user-cuda", "gpu", and "opt"
{gpu} suffix are as follows: 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 You can specify the accelerated styles explicitly in your input script
gpu"_fix_gpu.html command must be used. The fix controls the GPU by including their suffix, or you can use the "-suffix command-line
selection and initialization steps. 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 :line
@ -199,9 +201,8 @@ command"_run_style.html.
[Restrictions:] [Restrictions:]
This style is part of the "asphere" package. The styles with a {gpu} This style is part of the "asphere" package. It is only enabled if
suffix are part of the "gpu" package. They are only enabled if LAMMPS LAMMPS was built with that package. See the "Making
was built with those packages. See the "Making
LAMMPS"_Section_start.html#2_3 section for more info. LAMMPS"_Section_start.html#2_3 section for more info.
This pair style requires that atoms be ellipsoids as defined by the This pair style requires that atoms be ellipsoids as defined by the