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\documentclass[12pt]{article}
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\begin{document}
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\begin{eqnarray*}
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E_{i} & = & F_{\alpha} \left( \sum_{j \ne i} \rho(r_{ij}) \right) +
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\frac{1}{2} \sum_{j \ne i} \phi_{\alpha \beta} (r_{ij}) +
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\frac{1}{2} \sum_{i,s} \left( \mu_{i}^{s} \right)^2 +
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\sum_{i,s,t} \left( \lambda_{i}^{st} \right)^2 - \frac{1}{6} \nu_{i} \\
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\mu_{i}^{s} & = & \sum_{i \ne j} u(r_{ij}) r_{ij}^{s} \\
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\lambda_{i}^{st} & = & \sum_{i \ne j} w(r_{ij}) r_{ij}^{s} r_{ij}^{t} \\
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\nu_{i} & = & \sum_{s} \lambda_{i}^{ss}
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\end{eqnarray*}
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\end{document}
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|
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@ -17,15 +17,16 @@
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officially released in LAMMPS.
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</P>
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<P>Accelerated versions of various <A HREF = "pair_style.html">pair_style</A>,
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<A HREF = "fix.html">fix</A>, <A HREF = "compute.html">compute</A>, and other command have been
|
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added to LAMMPS, which will typically run faster than the standard
|
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non-accelerated version, if you have the appropriate hardware on your
|
||||
system.
|
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<A HREF = "fix.html">fixes</A>, <A HREF = "compute.html">computes</A>, and other commands have
|
||||
been added to LAMMPS, which will typically run faster than the
|
||||
standard non-accelerated versions, if you have the appropriate
|
||||
hardware on your system.
|
||||
</P>
|
||||
<P>The accelerated styles have the same name as the standard version,
|
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except that a suffix is appended. Otherwise, the syntax
|
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for the command is identical, and the numerical results it produces
|
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should also be identical, except for precision and round-off issues.
|
||||
<P>The accelerated styles have the same name as the standard styles,
|
||||
except that a suffix is appended. Otherwise, the syntax for the
|
||||
command is identical, their functionality is the same, and the
|
||||
numerical results it produces should also be identical, except for
|
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precision and round-off issues.
|
||||
</P>
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||||
<P>For example, all of these variants of the basic Lennard-Jones pair
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style exist in LAMMPS:
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|
|
@ -39,12 +40,12 @@ style exist in LAMMPS:
|
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styles can be invoked by specifying them explicitly in your input
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script. Or you can use the <A HREF = "Section_start.html#2_6">-suffix command-line
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switch</A> to invoke the accelerated versions
|
||||
automatically. See the <A HREF = "suffix.html">suffix</A> command for info on how
|
||||
to turn off/on the suffix associated with this switch within your
|
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input script.
|
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automatically, without changing your input script. The
|
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<A HREF = "suffix.html">suffix</A> command also allows you to set a suffix and to
|
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turn off/on the comand-line switch setting within your input script.
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</P>
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<P>Styles with an "opt" suffix are part of the OPT package and typically
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speed-up the pairwise portion of your simulation by 5-25%.
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speed-up the pairwise calculations of your simulation by 5-25%.
|
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</P>
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<P>Styles with a "gpu" or "cuda" suffix are part of the GPU or USER-CUDA
|
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packages, and can be run on NVIDIA GPUs associated with your CPUs.
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|
|
@ -58,10 +59,10 @@ and kspace sections.
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</P>
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<P>The following sections explain:
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</P>
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<UL><LI>how to install the accelerated packages
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<LI>what hardware and software they require
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<UL><LI>what hardware and software the accelerated styles require
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<LI>how to install the accelerated packages
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<LI>what kind of problems they run best on
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<LI>guidelines for how to use the accelerated packages to best advantage
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<LI>guidelines for how to use them to best advantage
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<LI>the kinds of speed-ups you can expect
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</UL>
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<P>The final section compares and contrasts the GPU and USER-CUDA
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|
|
@ -74,11 +75,32 @@ packages, since they are both designed to use NVIDIA GPU hardware.
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<HR>
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<HR>
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<H4><A NAME = "10_1"></A>10.1 OPT package
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</H4>
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<P>The OPT package was developed by James Fischer (High Performance
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Technologies), David Richie and Vincent Natoli (Stone Ridge
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Technologies).
|
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Technologies). It contains a handful of pair styles whose compute()
|
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methods were rewritten in C++ templated form to reduce the overhead
|
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due to if tests and other conditional code.
|
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</P>
|
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<P>The procedure for building LAMMPS with the OPT package is simple. It
|
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is the same as for any other package which has no additional library
|
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dependencies:
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</P>
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<PRE>make yes-opt
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make machine
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</PRE>
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<P>If your input script uses one of the OPT pair styles,
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you can run it as follows:
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</P>
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<PRE>lmp_machine -sf opt < in.script
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mpirun -np 4 lmp_machine -sf opt < in.script
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</PRE>
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<P>You should see a reduction in the "Pair time" printed out at the end
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of the run. On most machines and problems, this will typically be a 5
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to 20% savings.
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</P>
|
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<HR>
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|
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|
|
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|
|
@ -14,15 +14,16 @@ NOTE: The USER-CUDA package discussed below has not yet been
|
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officially released in LAMMPS.
|
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|
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Accelerated versions of various "pair_style"_pair_style.html,
|
||||
"fix"_fix.html, "compute"_compute.html, and other command have been
|
||||
added to LAMMPS, which will typically run faster than the standard
|
||||
non-accelerated version, if you have the appropriate hardware on your
|
||||
system.
|
||||
"fixes"_fix.html, "computes"_compute.html, and other commands have
|
||||
been added to LAMMPS, which will typically run faster than the
|
||||
standard non-accelerated versions, if you have the appropriate
|
||||
hardware on your system.
|
||||
|
||||
The accelerated styles have the same name as the standard version,
|
||||
except that a suffix is appended. Otherwise, the syntax
|
||||
for the command is identical, and the numerical results it produces
|
||||
should also be identical, except for precision and round-off issues.
|
||||
The accelerated styles have the same name as the standard styles,
|
||||
except that a suffix is appended. Otherwise, the syntax for the
|
||||
command is identical, their functionality is the same, and the
|
||||
numerical results it produces should also be identical, except for
|
||||
precision and round-off issues.
|
||||
|
||||
For example, all of these variants of the basic Lennard-Jones pair
|
||||
style exist in LAMMPS:
|
||||
|
|
@ -36,12 +37,12 @@ Assuming you have built LAMMPS with the appropriate package, these
|
|||
styles can be invoked by specifying them explicitly in your input
|
||||
script. Or you can use the "-suffix command-line
|
||||
switch"_Section_start.html#2_6 to invoke the accelerated versions
|
||||
automatically. See the "suffix"_suffix.html command for info on how
|
||||
to turn off/on the suffix associated with this switch within your
|
||||
input script.
|
||||
automatically, without changing your input script. The
|
||||
"suffix"_suffix.html command also allows you to set a suffix and to
|
||||
turn off/on the comand-line switch setting within your input script.
|
||||
|
||||
Styles with an "opt" suffix are part of the OPT package and typically
|
||||
speed-up the pairwise portion of your simulation by 5-25%.
|
||||
speed-up the pairwise calculations of your simulation by 5-25%.
|
||||
|
||||
Styles with a "gpu" or "cuda" suffix are part of the GPU or USER-CUDA
|
||||
packages, and can be run on NVIDIA GPUs associated with your CPUs.
|
||||
|
|
@ -55,10 +56,10 @@ and kspace sections.
|
|||
|
||||
The following sections explain:
|
||||
|
||||
what hardware and software the accelerated styles require
|
||||
how to install the accelerated packages
|
||||
what hardware and software they require
|
||||
what kind of problems they run best on
|
||||
guidelines for how to use the accelerated packages to best advantage
|
||||
guidelines for how to use them to best advantage
|
||||
the kinds of speed-ups you can expect :ul
|
||||
|
||||
The final section compares and contrasts the GPU and USER-CUDA
|
||||
|
|
@ -69,13 +70,33 @@ packages, since they are both designed to use NVIDIA GPU hardware.
|
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10.3 "USER-CUDA package"_#10_3
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10.4 "Comparison of GPU and USER-CUDA packages"_#10_4 :all(b)
|
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|
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:line
|
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:line
|
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|
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10.1 OPT package :h4,link(10_1)
|
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|
||||
The OPT package was developed by James Fischer (High Performance
|
||||
Technologies), David Richie and Vincent Natoli (Stone Ridge
|
||||
Technologies).
|
||||
Technologies). It contains a handful of pair styles whose compute()
|
||||
methods were rewritten in C++ templated form to reduce the overhead
|
||||
due to if tests and other conditional code.
|
||||
|
||||
The procedure for building LAMMPS with the OPT package is simple. It
|
||||
is the same as for any other package which has no additional library
|
||||
dependencies:
|
||||
|
||||
make yes-opt
|
||||
make machine :pre
|
||||
|
||||
If your input script uses one of the OPT pair styles,
|
||||
you can run it as follows:
|
||||
|
||||
lmp_machine -sf opt < in.script
|
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mpirun -np 4 lmp_machine -sf opt < in.script :pre
|
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|
||||
You should see a reduction in the "Pair time" printed out at the end
|
||||
of the run. On most machines and problems, this will typically be a 5
|
||||
to 20% savings.
|
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|
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:line
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|
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|
|
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|||
|
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@ -407,21 +407,22 @@ package</A>.
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potentials. Click on the style itself for a full description:
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</P>
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<DIV ALIGN=center><TABLE BORDER=1 >
|
||||
<TR ALIGN="center"><TD ><A HREF = "pair_none.html">none</A></TD><TD ><A HREF = "pair_hybrid.html">hybrid</A></TD><TD ><A HREF = "pair_hybrid.html">hybrid/overlay</A></TD><TD ><A HREF = "pair_airebo.html">airebo</A></TD></TR>
|
||||
<TR ALIGN="center"><TD ><A HREF = "pair_born.html">born</A></TD><TD ><A HREF = "pair_born.html">born/coul/long</A></TD><TD ><A HREF = "pair_buck.html">buck</A></TD><TD ><A HREF = "pair_buck.html">buck/coul/cut</A></TD></TR>
|
||||
<TR ALIGN="center"><TD ><A HREF = "pair_buck.html">buck/coul/long</A></TD><TD ><A HREF = "pair_colloid.html">colloid</A></TD><TD ><A HREF = "pair_comb.html">comb</A></TD><TD ><A HREF = "pair_coul.html">coul/cut</A></TD></TR>
|
||||
<TR ALIGN="center"><TD ><A HREF = "pair_coul.html">coul/debye</A></TD><TD ><A HREF = "pair_coul.html">coul/long</A></TD><TD ><A HREF = "pair_dipole.html">dipole/cut</A></TD><TD ><A HREF = "pair_dpd.html">dpd</A></TD></TR>
|
||||
<TR ALIGN="center"><TD ><A HREF = "pair_dpd.html">dpd/tstat</A></TD><TD ><A HREF = "pair_dsmc.html">dsmc</A></TD><TD ><A HREF = "pair_eam.html">eam</A></TD><TD ><A HREF = "pair_eam.html">eam/alloy</A></TD></TR>
|
||||
<TR ALIGN="center"><TD ><A HREF = "pair_eam.html">eam/fs</A></TD><TD ><A HREF = "pair_eim.html">eim</A></TD><TD ><A HREF = "pair_gauss.html">gauss</A></TD><TD ><A HREF = "pair_gayberne.html">gayberne</A></TD></TR>
|
||||
<TR ALIGN="center"><TD ><A HREF = "pair_gran.html">gran/hertz/history</A></TD><TD ><A HREF = "pair_gran.html">gran/hooke</A></TD><TD ><A HREF = "pair_gran.html">gran/hooke/history</A></TD><TD ><A HREF = "pair_hbond_dreiding.html">hbond/dreiding/lj</A></TD></TR>
|
||||
<TR ALIGN="center"><TD ><A HREF = "pair_hbond_dreiding.html">hbond/dreiding/morse</A></TD><TD ><A HREF = "pair_charmm.html">lj/charmm/coul/charmm</A></TD><TD ><A HREF = "pair_charmm.html">lj/charmm/coul/charmm/implicit</A></TD><TD ><A HREF = "pair_charmm.html">lj/charmm/coul/long</A></TD></TR>
|
||||
<TR ALIGN="center"><TD ><A HREF = "pair_class2.html">lj/class2</A></TD><TD ><A HREF = "pair_class2.html">lj/class2/coul/cut</A></TD><TD ><A HREF = "pair_class2.html">lj/class2/coul/long</A></TD><TD ><A HREF = "pair_lj.html">lj/cut</A></TD></TR>
|
||||
<TR ALIGN="center"><TD ><A HREF = "pair_lj.html">lj/cut/coul/cut</A></TD><TD ><A HREF = "pair_lj.html">lj/cut/coul/debye</A></TD><TD ><A HREF = "pair_lj.html">lj/cut/coul/long</A></TD><TD ><A HREF = "pair_lj.html">lj/cut/coul/long/tip4p</A></TD></TR>
|
||||
<TR ALIGN="center"><TD ><A HREF = "pair_lj_expand.html">lj/expand</A></TD><TD ><A HREF = "pair_gromacs.html">lj/gromacs</A></TD><TD ><A HREF = "pair_gromacs.html">lj/gromacs/coul/gromacs</A></TD><TD ><A HREF = "pair_lj_smooth.html">lj/smooth</A></TD></TR>
|
||||
<TR ALIGN="center"><TD ><A HREF = "pair_lj96.html">lj96/cut</A></TD><TD ><A HREF = "pair_lubricate.html">lubricate</A></TD><TD ><A HREF = "pair_meam.html">meam</A></TD><TD ><A HREF = "pair_morse.html">morse</A></TD></TR>
|
||||
<TR ALIGN="center"><TD ><A HREF = "pair_peri.html">peri/lps</A></TD><TD ><A HREF = "pair_peri.html">peri/pmb</A></TD><TD ><A HREF = "pair_reax.html">reax</A></TD><TD ><A HREF = "pair_airebo.html">rebo</A></TD></TR>
|
||||
<TR ALIGN="center"><TD ><A HREF = "pair_resquared.html">resquared</A></TD><TD ><A HREF = "pair_soft.html">soft</A></TD><TD ><A HREF = "pair_sw.html">sw</A></TD><TD ><A HREF = "pair_table.html">table</A></TD></TR>
|
||||
<TR ALIGN="center"><TD ><A HREF = "pair_tersoff.html">tersoff</A></TD><TD ><A HREF = "pair_tersoff_zbl.html">tersoff/zbl</A></TD><TD ><A HREF = "pair_yukawa.html">yukawa</A></TD><TD ><A HREF = "pair_yukawa_colloid.html">yukawa/colloid</A>
|
||||
<TR ALIGN="center"><TD ><A HREF = "pair_none.html">none</A></TD><TD ><A HREF = "pair_hybrid.html">hybrid</A></TD><TD ><A HREF = "pair_hybrid.html">hybrid/overlay</A></TD><TD ><A HREF = "pair_adp.html">adp</A></TD></TR>
|
||||
<TR ALIGN="center"><TD ><A HREF = "pair_airebo.html">airebo</A></TD><TD ><A HREF = "pair_born.html">born</A></TD><TD ><A HREF = "pair_born.html">born/coul/long</A></TD><TD ><A HREF = "pair_buck.html">buck</A></TD></TR>
|
||||
<TR ALIGN="center"><TD ><A HREF = "pair_buck.html">buck/coul/cut</A></TD><TD ><A HREF = "pair_buck.html">buck/coul/long</A></TD><TD ><A HREF = "pair_colloid.html">colloid</A></TD><TD ><A HREF = "pair_comb.html">comb</A></TD></TR>
|
||||
<TR ALIGN="center"><TD ><A HREF = "pair_coul.html">coul/cut</A></TD><TD ><A HREF = "pair_coul.html">coul/debye</A></TD><TD ><A HREF = "pair_coul.html">coul/long</A></TD><TD ><A HREF = "pair_dipole.html">dipole/cut</A></TD></TR>
|
||||
<TR ALIGN="center"><TD ><A HREF = "pair_dpd.html">dpd</A></TD><TD ><A HREF = "pair_dpd.html">dpd/tstat</A></TD><TD ><A HREF = "pair_dsmc.html">dsmc</A></TD><TD ><A HREF = "pair_eam.html">eam</A></TD></TR>
|
||||
<TR ALIGN="center"><TD ><A HREF = "pair_eam.html">eam/alloy</A></TD><TD ><A HREF = "pair_eam.html">eam/fs</A></TD><TD ><A HREF = "pair_eim.html">eim</A></TD><TD ><A HREF = "pair_gauss.html">gauss</A></TD></TR>
|
||||
<TR ALIGN="center"><TD ><A HREF = "pair_gayberne.html">gayberne</A></TD><TD ><A HREF = "pair_gran.html">gran/hertz/history</A></TD><TD ><A HREF = "pair_gran.html">gran/hooke</A></TD><TD ><A HREF = "pair_gran.html">gran/hooke/history</A></TD></TR>
|
||||
<TR ALIGN="center"><TD ><A HREF = "pair_hbond_dreiding.html">hbond/dreiding/lj</A></TD><TD ><A HREF = "pair_hbond_dreiding.html">hbond/dreiding/morse</A></TD><TD ><A HREF = "pair_charmm.html">lj/charmm/coul/charmm</A></TD><TD ><A HREF = "pair_charmm.html">lj/charmm/coul/charmm/implicit</A></TD></TR>
|
||||
<TR ALIGN="center"><TD ><A HREF = "pair_charmm.html">lj/charmm/coul/long</A></TD><TD ><A HREF = "pair_class2.html">lj/class2</A></TD><TD ><A HREF = "pair_class2.html">lj/class2/coul/cut</A></TD><TD ><A HREF = "pair_class2.html">lj/class2/coul/long</A></TD></TR>
|
||||
<TR ALIGN="center"><TD ><A HREF = "pair_lj.html">lj/cut</A></TD><TD ><A HREF = "pair_lj.html">lj/cut/coul/cut</A></TD><TD ><A HREF = "pair_lj.html">lj/cut/coul/debye</A></TD><TD ><A HREF = "pair_lj.html">lj/cut/coul/long</A></TD></TR>
|
||||
<TR ALIGN="center"><TD ><A HREF = "pair_lj.html">lj/cut/coul/long/tip4p</A></TD><TD ><A HREF = "pair_lj_expand.html">lj/expand</A></TD><TD ><A HREF = "pair_gromacs.html">lj/gromacs</A></TD><TD ><A HREF = "pair_gromacs.html">lj/gromacs/coul/gromacs</A></TD></TR>
|
||||
<TR ALIGN="center"><TD ><A HREF = "pair_lj_smooth.html">lj/smooth</A></TD><TD ><A HREF = "pair_lj96.html">lj96/cut</A></TD><TD ><A HREF = "pair_lubricate.html">lubricate</A></TD><TD ><A HREF = "pair_meam.html">meam</A></TD></TR>
|
||||
<TR ALIGN="center"><TD ><A HREF = "pair_morse.html">morse</A></TD><TD ><A HREF = "pair_peri.html">peri/lps</A></TD><TD ><A HREF = "pair_peri.html">peri/pmb</A></TD><TD ><A HREF = "pair_reax.html">reax</A></TD></TR>
|
||||
<TR ALIGN="center"><TD ><A HREF = "pair_airebo.html">rebo</A></TD><TD ><A HREF = "pair_resquared.html">resquared</A></TD><TD ><A HREF = "pair_soft.html">soft</A></TD><TD ><A HREF = "pair_sw.html">sw</A></TD></TR>
|
||||
<TR ALIGN="center"><TD ><A HREF = "pair_table.html">table</A></TD><TD ><A HREF = "pair_tersoff.html">tersoff</A></TD><TD ><A HREF = "pair_tersoff_zbl.html">tersoff/zbl</A></TD><TD ><A HREF = "pair_yukawa.html">yukawa</A></TD></TR>
|
||||
<TR ALIGN="center"><TD ><A HREF = "pair_yukawa_colloid.html">yukawa/colloid</A>
|
||||
</TD></TR></TABLE></DIV>
|
||||
|
||||
<P>These are pair styles contributed by users, which can be used if
|
||||
|
|
@ -441,14 +442,14 @@ package</A>.
|
|||
<TR ALIGN="center"><TD ><A HREF = "pair_cmm.html">cg/cmm/cuda</A></TD><TD ><A HREF = "pair_cmm.html">cg/cmm/coul/cut/cuda</A></TD><TD ><A HREF = "pair_cmm.html">cg/cmm/coul/debye/cuda</A></TD><TD ><A HREF = "pair_cmm.html">cg/cmm/coul/long/cuda</A></TD></TR>
|
||||
<TR ALIGN="center"><TD ><A HREF = "pair_lj.html">lj/cut/coul/long/cuda</A></TD><TD ><A HREF = "pair_eam.html">eam/alloy/cuda</A></TD><TD ><A HREF = "pair_eam.html">eam/cuda</A></TD><TD ><A HREF = "pair_eam.html">eam/fs/cuda</A></TD></TR>
|
||||
<TR ALIGN="center"><TD ><A HREF = "pair_gran.html">gran/hooke/cuda</A></TD><TD ><A HREF = "pair_charmm.html">lj/charmm/coul/charmm/cuda</A></TD><TD ><A HREF = "pair_charmm.html">lj/charmm/coul/charmm/implicit/cuda</A></TD><TD ><A HREF = "pair_charmm.html">lj/charmm/coul/long/cuda</A></TD></TR>
|
||||
<TR ALIGN="center"><TD ><A HREF = "pair_class2.html">lj/class2/coul/cut/cuda</A></TD><TD ><A HREF = "pair_class2.html">lj/class2/cuda</A></TD><TD ><A HREF = "pair_class2.html">lj/class2/coul/long/cuda</A></TD><TD ><A HREF = "pair_lj.html">lj/cut/coul/cut/cuda</A></TD></TR>
|
||||
<TR ALIGN="center"><TD ><A HREF = "pair_lj.html">lj/cut/coul/debye/cuda</A></TD><TD ><A HREF = "pair_lj.html">lj/cut/cuda</A></TD><TD ><A HREF = "pair_lj.html">lj/cut/experimental/cuda</A></TD><TD ><A HREF = "pair_lj_expand.html">lj/expand/cuda</A></TD></TR>
|
||||
<TR ALIGN="center"><TD ><A HREF = "pair_gromacs.html">lj/gromacs/coul/gromacs/cuda</A></TD><TD ><A HREF = "pair_gromacs.html">lj/gromacs/cuda</A></TD><TD ><A HREF = "pair_lj_smooth.html">lj/smooth/cuda</A></TD><TD ><A HREF = "pair_lj96.html">lj96/cut/cuda</A></TD></TR>
|
||||
<TR ALIGN="center"><TD ><A HREF = "pair_morse.html">morse/cuda</A></TD><TD ><A HREF = "pair_gayberne.html">gayberne/gpu</A></TD><TD ><A HREF = "pair_cmm.html">cg/cmm/gpu</A></TD><TD ><A HREF = "pair_cmm.html">cg/cmm/coul/long/gpu</A></TD></TR>
|
||||
<TR ALIGN="center"><TD ><A HREF = "pair_charmm.html">lj/charmm/coul/long/gpu</A></TD><TD ><A HREF = "pair_lj.html">lj/cut/coul/cut/gpu</A></TD><TD ><A HREF = "pair_lj.html">lj/cut/coul/long/gpu</A></TD><TD ><A HREF = "pair_lj.html">lj/cut/gpu</A></TD></TR>
|
||||
<TR ALIGN="center"><TD ><A HREF = "pair_lj_expand.html">lj/expand/gpu</A></TD><TD ><A HREF = "pair_lj96.html">lj96/cut/gpu</A></TD><TD ><A HREF = "pair_morse.html">morse/gpu</A></TD><TD ><A HREF = "pair_eam.html">eam/opt</A></TD></TR>
|
||||
<TR ALIGN="center"><TD ><A HREF = "pair_eam.html">eam/alloy/opt</A></TD><TD ><A HREF = "pair_eam.html">eam/fs/opt</A></TD><TD ><A HREF = "pair_charmm.html">lj/charmm/coul/long/opt</A></TD><TD ><A HREF = "pair_lj.html">lj/cut/opt</A></TD></TR>
|
||||
<TR ALIGN="center"><TD ><A HREF = "pair_morse.html">morse/opt</A>
|
||||
<TR ALIGN="center"><TD ><A HREF = "pair_class2.html">lj/class2/coul/cut/cuda</A></TD><TD ><A HREF = "pair_class2.html">lj/class2/cuda</A></TD><TD ><A HREF = "pair_class2.html">lj/class2/gpu</A></TD><TD ><A HREF = "pair_class2.html">lj/class2/coul/long/cuda</A></TD></TR>
|
||||
<TR ALIGN="center"><TD ><A HREF = "pair_class2.html">lj/class2/coul/long/gpu</A></TD><TD ><A HREF = "pair_lj.html">lj/cut/coul/cut/cuda</A></TD><TD ><A HREF = "pair_lj.html">lj/cut/coul/debye/cuda</A></TD><TD ><A HREF = "pair_lj.html">lj/cut/cuda</A></TD></TR>
|
||||
<TR ALIGN="center"><TD ><A HREF = "pair_lj.html">lj/cut/experimental/cuda</A></TD><TD ><A HREF = "pair_lj_expand.html">lj/expand/cuda</A></TD><TD ><A HREF = "pair_gromacs.html">lj/gromacs/coul/gromacs/cuda</A></TD><TD ><A HREF = "pair_gromacs.html">lj/gromacs/cuda</A></TD></TR>
|
||||
<TR ALIGN="center"><TD ><A HREF = "pair_lj_smooth.html">lj/smooth/cuda</A></TD><TD ><A HREF = "pair_lj96.html">lj96/cut/cuda</A></TD><TD ><A HREF = "pair_morse.html">morse/cuda</A></TD><TD ><A HREF = "pair_gayberne.html">gayberne/gpu</A></TD></TR>
|
||||
<TR ALIGN="center"><TD ><A HREF = "pair_cmm.html">cg/cmm/gpu</A></TD><TD ><A HREF = "pair_cmm.html">cg/cmm/coul/long/gpu</A></TD><TD ><A HREF = "pair_charmm.html">lj/charmm/coul/long/gpu</A></TD><TD ><A HREF = "pair_lj.html">lj/cut/coul/cut/gpu</A></TD></TR>
|
||||
<TR ALIGN="center"><TD ><A HREF = "pair_lj.html">lj/cut/coul/long/gpu</A></TD><TD ><A HREF = "pair_lj.html">lj/cut/gpu</A></TD><TD ><A HREF = "pair_lj_expand.html">lj/expand/gpu</A></TD><TD ><A HREF = "pair_lj96.html">lj96/cut/gpu</A></TD></TR>
|
||||
<TR ALIGN="center"><TD ><A HREF = "pair_morse.html">morse/gpu</A></TD><TD ><A HREF = "pair_eam.html">eam/opt</A></TD><TD ><A HREF = "pair_eam.html">eam/alloy/opt</A></TD><TD ><A HREF = "pair_eam.html">eam/fs/opt</A></TD></TR>
|
||||
<TR ALIGN="center"><TD ><A HREF = "pair_charmm.html">lj/charmm/coul/long/opt</A></TD><TD ><A HREF = "pair_lj.html">lj/cut/opt</A></TD><TD ><A HREF = "pair_morse.html">morse/opt</A></TD><TD ><A HREF = "pair_resquared.html">resquared/gpu</A>
|
||||
</TD></TR></TABLE></DIV>
|
||||
|
||||
<HR>
|
||||
|
|
|
|||
|
|
@ -595,6 +595,7 @@ potentials. Click on the style itself for a full description:
|
|||
"none"_pair_none.html,
|
||||
"hybrid"_pair_hybrid.html,
|
||||
"hybrid/overlay"_pair_hybrid.html,
|
||||
"adp"_pair_adp.html,
|
||||
"airebo"_pair_airebo.html,
|
||||
"born"_pair_born.html,
|
||||
"born/coul/long"_pair_born.html,
|
||||
|
|
@ -687,7 +688,9 @@ package"_Section_accelerate.html.
|
|||
"lj/charmm/coul/long/cuda"_pair_charmm.html,
|
||||
"lj/class2/coul/cut/cuda"_pair_class2.html,
|
||||
"lj/class2/cuda"_pair_class2.html,
|
||||
"lj/class2/gpu"_pair_class2.html,
|
||||
"lj/class2/coul/long/cuda"_pair_class2.html,
|
||||
"lj/class2/coul/long/gpu"_pair_class2.html,
|
||||
"lj/cut/coul/cut/cuda"_pair_lj.html,
|
||||
"lj/cut/coul/debye/cuda"_pair_lj.html,
|
||||
"lj/cut/cuda"_pair_lj.html,
|
||||
|
|
@ -713,7 +716,8 @@ package"_Section_accelerate.html.
|
|||
"eam/fs/opt"_pair_eam.html,
|
||||
"lj/charmm/coul/long/opt"_pair_charmm.html,
|
||||
"lj/cut/opt"_pair_lj.html,
|
||||
"morse/opt"_pair_morse.html :tb(c=4,ea=c)
|
||||
"morse/opt"_pair_morse.html,
|
||||
"resquared/gpu"_pair_resquared.html :tb(c=4,ea=c)
|
||||
|
||||
:line
|
||||
|
||||
|
|
|
|||
|
|
@ -139,7 +139,7 @@ commands)
|
|||
</P>
|
||||
<UL><LI> pairwise potentials: Lennard-Jones, Buckingham, Morse, Born-Mayer-Huggins, Yukawa, soft, class 2 (COMPASS), hydrogen bond, tabulated
|
||||
<LI> charged pairwise potentials: Coulombic, point-dipole
|
||||
<LI> manybody potentials: EAM, Finnis/Sinclair EAM, modified EAM (MEAM), embedded ion method (EIM), Stillinger-Weber, Tersoff, REBO, AIREBO, ReaxFF, COMB
|
||||
<LI> manybody potentials: EAM, Finnis/Sinclair EAM, modified EAM (MEAM), embedded ion method (EIM), ADP, Stillinger-Weber, Tersoff, REBO, AIREBO, ReaxFF, COMB
|
||||
<LI> electron force field (eFF)
|
||||
<LI> coarse-grained potentials: DPD, GayBerne, REsquared, colloidal, DLVO
|
||||
<LI> mesoscopic potentials: granular, Peridynamics
|
||||
|
|
|
|||
|
|
@ -136,7 +136,7 @@ commands)
|
|||
Yukawa, soft, class 2 (COMPASS), hydrogen bond, tabulated
|
||||
charged pairwise potentials: Coulombic, point-dipole
|
||||
manybody potentials: EAM, Finnis/Sinclair EAM, modified EAM (MEAM), \
|
||||
embedded ion method (EIM), Stillinger-Weber, Tersoff, REBO, AIREBO, ReaxFF, COMB
|
||||
embedded ion method (EIM), ADP, Stillinger-Weber, Tersoff, REBO, AIREBO, ReaxFF, COMB
|
||||
electron force field (eFF)
|
||||
coarse-grained potentials: DPD, GayBerne, REsquared, colloidal, DLVO
|
||||
mesoscopic potentials: granular, Peridynamics
|
||||
|
|
|
|||
|
|
@ -223,9 +223,9 @@ Restrictions section of the <A HREF = "dump.html">dump</A> command for details.
|
|||
</P>
|
||||
<P>If you use -DLAMMPS_JPEG, the <A HREF = "dump.html">dump image</A> command will be
|
||||
able to write out JPEG image files. If not, it will only be able to
|
||||
write out PPM image files. For JPEG files, you must also link LAMMPS
|
||||
with a JPEG library. See section (3.d) below for more details on
|
||||
this.
|
||||
write out text-based PPM image files. For JPEG files, you must also
|
||||
link LAMMPS with a JPEG library. See section (3.d) below for more
|
||||
details on this.
|
||||
</P>
|
||||
<P>(3.b) The 3 MPI variables are used to specify an MPI library to build
|
||||
LAMMPS with.
|
||||
|
|
|
|||
|
|
@ -218,9 +218,9 @@ Restrictions section of the "dump"_dump.html command for details.
|
|||
|
||||
If you use -DLAMMPS_JPEG, the "dump image"_dump.html command will be
|
||||
able to write out JPEG image files. If not, it will only be able to
|
||||
write out PPM image files. For JPEG files, you must also link LAMMPS
|
||||
with a JPEG library. See section (3.d) below for more details on
|
||||
this.
|
||||
write out text-based PPM image files. For JPEG files, you must also
|
||||
link LAMMPS with a JPEG library. See section (3.d) below for more
|
||||
details on this.
|
||||
|
||||
(3.b) The 3 MPI variables are used to specify an MPI library to build
|
||||
LAMMPS with.
|
||||
|
|
|
|||
|
|
@ -11,8 +11,6 @@
|
|||
|
||||
<H3>dump image command
|
||||
</H3>
|
||||
<P>NOTE: The dump image command has not yet been released as part of LAMMPS.
|
||||
</P>
|
||||
<P><B>Syntax:</B>
|
||||
</P>
|
||||
<PRE>dump ID group-ID image N file color diameter keyword value ...
|
||||
|
|
@ -38,8 +36,8 @@
|
|||
<PRE> <I>adiam</I> value = number = numeric value for atom diameter (distance units)
|
||||
<I>atom</I> = yes/no = do or do not draw atoms
|
||||
<I>bond</I> values = color width = color and width of bonds
|
||||
color = <I>atom</I> or <I>type</I>
|
||||
width = number or <I>atom</I> or <I>type</I>
|
||||
color = <I>atom</I> or <I>type</I> or <I>none</I>
|
||||
width = number or <I>atom</I> or <I>type</I> or <I>none</I>
|
||||
number = numeric value for bond width (distance units)
|
||||
<I>size</I> values = width height = size of images
|
||||
width = width of image in # of pixels
|
||||
|
|
@ -55,12 +53,12 @@
|
|||
<I>up</I> values = Ux Uy Uz = direction that is "up" in image
|
||||
Ux,Uy,Uz = components of up vector
|
||||
Ux,Uy,Uz can be variables (see below)
|
||||
<I>zoom</I> value = factor = size that simulation box appears in image
|
||||
factor = scale image size by factor > 1 to enlarge, factor < 1 to shrink
|
||||
factor can be a variable (see below)
|
||||
<I>persp</I> value = factor = amount of "perspective" in image
|
||||
factor = amount of perspective (0 = none, < 1 = some, > 1 = highly skewed)
|
||||
factor can be a variable (see below)
|
||||
<I>zoom</I> value = zfactor = size that simulation box appears in image
|
||||
zfactor = scale image size by factor > 1 to enlarge, factor < 1 to shrink
|
||||
zfactor can be a variable (see below)
|
||||
<I>persp</I> value = pfactor = amount of "perspective" in image
|
||||
pfactor = amount of perspective (0 = none, < 1 = some, > 1 = highly skewed)
|
||||
pfactor can be a variable (see below)
|
||||
<I>box</I> values = yes/no diam = draw outline of simulation box
|
||||
yes/no = do or do not draw simulation box lines
|
||||
diam = diameter of box lines as fraction of shortest box length
|
||||
|
|
@ -68,8 +66,8 @@
|
|||
yes/no = do or do not draw xyz axes lines next to simulation box
|
||||
length = length of axes lines as fraction of respective box lengths
|
||||
diam = diameter of axes lines as fraction of shortest box length
|
||||
<I>shiny</I> value = factor = shinyness of spheres and cylinders
|
||||
factor = shinyness of spheres and cylinders from 0.0 to 1.0
|
||||
<I>shiny</I> value = sfactor = shinyness of spheres and cylinders
|
||||
sfactor = shinyness of spheres and cylinders from 0.0 to 1.0
|
||||
<I>ssao</I> value = yes/no seed = SSAO depth shading
|
||||
yes/no = turn depth shading on/off
|
||||
seed = random # seed (positive integer)
|
||||
|
|
@ -205,12 +203,14 @@ drawn with that diameter, e.g. 1.5, which is in whatever distance
|
|||
<P>The <I>atom</I> keyword allow you to turn off the drawing of all atoms,
|
||||
if the specified value is <I>no</I>.
|
||||
</P>
|
||||
<P>By default, no bonds between atoms are drawn in the renedered image.
|
||||
The <I>bond</I> keyword cause bonds between pairs of atoms (as defined in
|
||||
the data file read by the <A HREF = "read_data.html">read_data</A> command) to be
|
||||
drawn with the specified color and width. A bond is only drawn if
|
||||
both atoms in the bond are part of the group specified with the dump
|
||||
image command.
|
||||
<P>The <I>bond</I> keyword allows to you to alter how bonds are drawn. A bond
|
||||
is only drawn if both atoms in the bond are being drawn due to being
|
||||
in the specified group and due to other selection criteria
|
||||
(e.g. region, threshhold settings of the
|
||||
<A HREF = "dump_modify.html">dump_modify</A> command). By default, bonds are drawn
|
||||
if they are defined in the input data file as read by the
|
||||
<A HREF = "read_data.html">read_data</A> command. Using <I>none</I> for both the bond
|
||||
<I>color</I> and <I>width</I> value will turn off the drawing of all bonds.
|
||||
</P>
|
||||
<P>If <I>atom</I> is specified for the bond <I>color</I> value, then each bond is
|
||||
drawn in 2 halves, with the color of each half being the color of the
|
||||
|
|
@ -230,7 +230,8 @@ types to colors is as follows:
|
|||
<P>and repeats itself for bond types > 6. This mapping can be changed by
|
||||
the <A HREF = "dump_modify.html">dump_modify bcolor</A> command.
|
||||
</P>
|
||||
<P>The bond <I>width</I> value can be a numeric value or <I>atom</I> or <I>type</I>.
|
||||
<P>The bond <I>width</I> value can be a numeric value or <I>atom</I> or <I>type</I> (or
|
||||
<I>none</I> as indicated above).
|
||||
</P>
|
||||
<P>If a numeric value is specified, then all bonds will be drawn as
|
||||
cylinders with that diameter, e.g. 1.0, which is in whatever distance
|
||||
|
|
@ -271,7 +272,9 @@ box is viewed, looking towards the <I>center</I> point. The <I>theta</I> value
|
|||
is the vertical angle from the +z axis, and must be an angle from 0 to
|
||||
180 degrees. The <I>phi</I> value is an azimuthal angle around the z axis
|
||||
and can be positive or negative. A value of 0.0 is a view along the
|
||||
+x axis, towards the <I>center</I> point.
|
||||
+x axis, towards the <I>center</I> point. If <I>theta</I> or <I>phi</I> are
|
||||
specified via variables, then the variable values should be in
|
||||
degrees.
|
||||
</P>
|
||||
<P>The <I>center</I> keyword determines the point in simulation space that
|
||||
will be at the center of the image. <I>Cx</I>, <I>Cy</I>, and <I>Cz</I> are
|
||||
|
|
@ -301,20 +304,22 @@ it cannot be parallel to the <I>view</I> vector, implied by the <I>theta</I> and
|
|||
<I>phi</I> values.
|
||||
</P>
|
||||
<P>The <I>zoom</I> keyword scales the size of the simulation box as it appears
|
||||
in the image. The default <I>factor</I> value of 1 should display an
|
||||
image mostly filled by the atoms in the simulation box. A <I>factor</I> >
|
||||
1 will make the simulation box larger; a <I>factor</I> < 1 will make it
|
||||
smaller. <I>Factor</I> must be a value > 0.0.
|
||||
in the image. The default <I>zfactor</I> value of 1 should display an
|
||||
image mostly filled by the atoms in the simulation box. A <I>zfactor</I> >
|
||||
1 will make the simulation box larger; a <I>zfactor</I> < 1 will make it
|
||||
smaller. <I>Zfactor</I> must be a value > 0.0.
|
||||
</P>
|
||||
<P>The <I>persp</I> keyword determines how much depth perspective is present
|
||||
in the image. Depth perspective makes lines that are parallel in
|
||||
simulation space appear non-parallel in the image. A <I>factor</I> value
|
||||
of 0.0 means that parallel lines will meet at infininty (1.0/factor),
|
||||
which is an orthographic rendering with no persepctive. A <I>factor</I>
|
||||
value between 0.0 and 1.0 will introduce more perspective. A <I>factor</I>
|
||||
simulation space appear non-parallel in the image. A <I>pfactor</I> value
|
||||
of 0.0 means that parallel lines will meet at infininty (1.0/pfactor),
|
||||
which is an orthographic rendering with no persepctive. A <I>pfactor</I>
|
||||
value between 0.0 and 1.0 will introduce more perspective. A <I>pfactor</I>
|
||||
value > 1 will create a highly skewed image with a large amount of
|
||||
perspective.
|
||||
</P>
|
||||
<P>IMPORTANT NOTE: The <I>persp</I> keyword is not yet supported as an option.
|
||||
</P>
|
||||
<HR>
|
||||
|
||||
<P>The <I>box</I> keyword determines how the simulation box boundaries are
|
||||
|
|
@ -338,9 +343,9 @@ of the shortest box length in x,y,z (for 3d) or x,y (for 2d).
|
|||
<HR>
|
||||
|
||||
<P>The <I>shiny</I> keyword determines how shiny the objects rendered in the
|
||||
image will appear. The factor value must be a value 0.0 <= factor <=
|
||||
1.0, where factor = 1 is a highly reflective surface and factor = 0 is
|
||||
a rough non-shiny surface.
|
||||
image will appear. The <I>sfactor</I> value must be a value 0.0 <=
|
||||
<I>sfactor</I> <= 1.0, where <I>sfactor</I> = 1 is a highly reflective surface
|
||||
and <I>sfactor</I> = 0 is a rough non-shiny surface.
|
||||
</P>
|
||||
<P>The <I>ssao</I> keyword turns on/off a screen space ambient occlusion
|
||||
(SSAO) model for depth shading. If <I>yes</I> is set, then atoms further
|
||||
|
|
@ -418,7 +423,7 @@ details.
|
|||
<P>The defaults for the keywords are as follows:
|
||||
</P>
|
||||
<UL><LI>atom = type 1.0
|
||||
<LI>bond = none 0.0 (if no bonds in system)
|
||||
<LI>bond = none none (if no bonds in system)
|
||||
<LI>bond = atom 0.5 (if bonds in system)
|
||||
<LI>size = 512 512
|
||||
<LI>view = 60 30 (for 3d)
|
||||
|
|
@ -428,7 +433,7 @@ details.
|
|||
<LI>up = 0 1 0 (for 2d)
|
||||
<LI>zoom = 1.0
|
||||
<LI>persp = 0.0
|
||||
<LI>box = yes 0.01
|
||||
<LI>box = yes 0.02
|
||||
<LI>axes = no 0.0 0.0
|
||||
<LI>shiny = 1.0
|
||||
<LI>ssao = no
|
||||
|
|
|
|||
|
|
@ -8,8 +8,6 @@
|
|||
|
||||
dump image command :h3
|
||||
|
||||
NOTE: The dump image command has not yet been released as part of LAMMPS.
|
||||
|
||||
[Syntax:]
|
||||
|
||||
dump ID group-ID image N file color diameter keyword value ... :pre
|
||||
|
|
@ -26,8 +24,8 @@ keyword = {adiam} or {atom} or {bond} or {size} or {view} or {center} or {up} or
|
|||
{adiam} value = number = numeric value for atom diameter (distance units)
|
||||
{atom} = yes/no = do or do not draw atoms
|
||||
{bond} values = color width = color and width of bonds
|
||||
color = {atom} or {type}
|
||||
width = number or {atom} or {type}
|
||||
color = {atom} or {type} or {none}
|
||||
width = number or {atom} or {type} or {none}
|
||||
number = numeric value for bond width (distance units)
|
||||
{size} values = width height = size of images
|
||||
width = width of image in # of pixels
|
||||
|
|
@ -43,12 +41,12 @@ keyword = {adiam} or {atom} or {bond} or {size} or {view} or {center} or {up} or
|
|||
{up} values = Ux Uy Uz = direction that is "up" in image
|
||||
Ux,Uy,Uz = components of up vector
|
||||
Ux,Uy,Uz can be variables (see below)
|
||||
{zoom} value = factor = size that simulation box appears in image
|
||||
factor = scale image size by factor > 1 to enlarge, factor < 1 to shrink
|
||||
factor can be a variable (see below)
|
||||
{persp} value = factor = amount of "perspective" in image
|
||||
factor = amount of perspective (0 = none, < 1 = some, > 1 = highly skewed)
|
||||
factor can be a variable (see below)
|
||||
{zoom} value = zfactor = size that simulation box appears in image
|
||||
zfactor = scale image size by factor > 1 to enlarge, factor < 1 to shrink
|
||||
zfactor can be a variable (see below)
|
||||
{persp} value = pfactor = amount of "perspective" in image
|
||||
pfactor = amount of perspective (0 = none, < 1 = some, > 1 = highly skewed)
|
||||
pfactor can be a variable (see below)
|
||||
{box} values = yes/no diam = draw outline of simulation box
|
||||
yes/no = do or do not draw simulation box lines
|
||||
diam = diameter of box lines as fraction of shortest box length
|
||||
|
|
@ -56,8 +54,8 @@ keyword = {adiam} or {atom} or {bond} or {size} or {view} or {center} or {up} or
|
|||
yes/no = do or do not draw xyz axes lines next to simulation box
|
||||
length = length of axes lines as fraction of respective box lengths
|
||||
diam = diameter of axes lines as fraction of shortest box length
|
||||
{shiny} value = factor = shinyness of spheres and cylinders
|
||||
factor = shinyness of spheres and cylinders from 0.0 to 1.0
|
||||
{shiny} value = sfactor = shinyness of spheres and cylinders
|
||||
sfactor = shinyness of spheres and cylinders from 0.0 to 1.0
|
||||
{ssao} value = yes/no seed = SSAO depth shading
|
||||
yes/no = turn depth shading on/off
|
||||
seed = random # seed (positive integer) :pre
|
||||
|
|
@ -192,12 +190,14 @@ drawn with that diameter, e.g. 1.5, which is in whatever distance
|
|||
The {atom} keyword allow you to turn off the drawing of all atoms,
|
||||
if the specified value is {no}.
|
||||
|
||||
By default, no bonds between atoms are drawn in the renedered image.
|
||||
The {bond} keyword cause bonds between pairs of atoms (as defined in
|
||||
the data file read by the "read_data"_read_data.html command) to be
|
||||
drawn with the specified color and width. A bond is only drawn if
|
||||
both atoms in the bond are part of the group specified with the dump
|
||||
image command.
|
||||
The {bond} keyword allows to you to alter how bonds are drawn. A bond
|
||||
is only drawn if both atoms in the bond are being drawn due to being
|
||||
in the specified group and due to other selection criteria
|
||||
(e.g. region, threshhold settings of the
|
||||
"dump_modify"_dump_modify.html command). By default, bonds are drawn
|
||||
if they are defined in the input data file as read by the
|
||||
"read_data"_read_data.html command. Using {none} for both the bond
|
||||
{color} and {width} value will turn off the drawing of all bonds.
|
||||
|
||||
If {atom} is specified for the bond {color} value, then each bond is
|
||||
drawn in 2 halves, with the color of each half being the color of the
|
||||
|
|
@ -217,7 +217,8 @@ type 6 = cyan :ul
|
|||
and repeats itself for bond types > 6. This mapping can be changed by
|
||||
the "dump_modify bcolor"_dump_modify.html command.
|
||||
|
||||
The bond {width} value can be a numeric value or {atom} or {type}.
|
||||
The bond {width} value can be a numeric value or {atom} or {type} (or
|
||||
{none} as indicated above).
|
||||
|
||||
If a numeric value is specified, then all bonds will be drawn as
|
||||
cylinders with that diameter, e.g. 1.0, which is in whatever distance
|
||||
|
|
@ -258,7 +259,9 @@ box is viewed, looking towards the {center} point. The {theta} value
|
|||
is the vertical angle from the +z axis, and must be an angle from 0 to
|
||||
180 degrees. The {phi} value is an azimuthal angle around the z axis
|
||||
and can be positive or negative. A value of 0.0 is a view along the
|
||||
+x axis, towards the {center} point.
|
||||
+x axis, towards the {center} point. If {theta} or {phi} are
|
||||
specified via variables, then the variable values should be in
|
||||
degrees.
|
||||
|
||||
The {center} keyword determines the point in simulation space that
|
||||
will be at the center of the image. {Cx}, {Cy}, and {Cz} are
|
||||
|
|
@ -288,20 +291,22 @@ it cannot be parallel to the {view} vector, implied by the {theta} and
|
|||
{phi} values.
|
||||
|
||||
The {zoom} keyword scales the size of the simulation box as it appears
|
||||
in the image. The default {factor} value of 1 should display an
|
||||
image mostly filled by the atoms in the simulation box. A {factor} >
|
||||
1 will make the simulation box larger; a {factor} < 1 will make it
|
||||
smaller. {Factor} must be a value > 0.0.
|
||||
in the image. The default {zfactor} value of 1 should display an
|
||||
image mostly filled by the atoms in the simulation box. A {zfactor} >
|
||||
1 will make the simulation box larger; a {zfactor} < 1 will make it
|
||||
smaller. {Zfactor} must be a value > 0.0.
|
||||
|
||||
The {persp} keyword determines how much depth perspective is present
|
||||
in the image. Depth perspective makes lines that are parallel in
|
||||
simulation space appear non-parallel in the image. A {factor} value
|
||||
of 0.0 means that parallel lines will meet at infininty (1.0/factor),
|
||||
which is an orthographic rendering with no persepctive. A {factor}
|
||||
value between 0.0 and 1.0 will introduce more perspective. A {factor}
|
||||
simulation space appear non-parallel in the image. A {pfactor} value
|
||||
of 0.0 means that parallel lines will meet at infininty (1.0/pfactor),
|
||||
which is an orthographic rendering with no persepctive. A {pfactor}
|
||||
value between 0.0 and 1.0 will introduce more perspective. A {pfactor}
|
||||
value > 1 will create a highly skewed image with a large amount of
|
||||
perspective.
|
||||
|
||||
IMPORTANT NOTE: The {persp} keyword is not yet supported as an option.
|
||||
|
||||
:line
|
||||
|
||||
The {box} keyword determines how the simulation box boundaries are
|
||||
|
|
@ -325,9 +330,9 @@ of the shortest box length in x,y,z (for 3d) or x,y (for 2d).
|
|||
:line
|
||||
|
||||
The {shiny} keyword determines how shiny the objects rendered in the
|
||||
image will appear. The factor value must be a value 0.0 <= factor <=
|
||||
1.0, where factor = 1 is a highly reflective surface and factor = 0 is
|
||||
a rough non-shiny surface.
|
||||
image will appear. The {sfactor} value must be a value 0.0 <=
|
||||
{sfactor} <= 1.0, where {sfactor} = 1 is a highly reflective surface
|
||||
and {sfactor} = 0 is a rough non-shiny surface.
|
||||
|
||||
The {ssao} keyword turns on/off a screen space ambient occlusion
|
||||
(SSAO) model for depth shading. If {yes} is set, then atoms further
|
||||
|
|
@ -405,7 +410,7 @@ details.
|
|||
The defaults for the keywords are as follows:
|
||||
|
||||
atom = type 1.0
|
||||
bond = none 0.0 (if no bonds in system)
|
||||
bond = none none (if no bonds in system)
|
||||
bond = atom 0.5 (if bonds in system)
|
||||
size = 512 512
|
||||
view = 60 30 (for 3d)
|
||||
|
|
@ -415,7 +420,7 @@ up = 0 0 1 (for 3d)
|
|||
up = 0 1 0 (for 2d)
|
||||
zoom = 1.0
|
||||
persp = 0.0
|
||||
box = yes 0.01
|
||||
box = yes 0.02
|
||||
axes = no 0.0 0.0
|
||||
shiny = 1.0
|
||||
ssao = no :ul
|
||||
|
|
|
|||
|
|
@ -11,10 +11,6 @@
|
|||
|
||||
<H3>dump_modify command
|
||||
</H3>
|
||||
<P>NOTE: The keywords below which are only relevant for the <A HREF = "dump_image.html">dump
|
||||
image</A> command have not yet been released as part of
|
||||
LAMMPS.
|
||||
</P>
|
||||
<P><B>Syntax:</B>
|
||||
</P>
|
||||
<PRE>dump_modify dump-ID keyword values ...
|
||||
|
|
@ -103,7 +99,7 @@ dump_modify xtcdump precision 10000
|
|||
dump_modify 1 every 1000
|
||||
dump_modify 1 every v_myVar
|
||||
</PRE>
|
||||
<PRE>NOTE: need to add some image examples
|
||||
<PRE>dump_modify 1 amap min max cf 0.0 3 min green 0.5 yellow max blue boxcolor red
|
||||
</PRE>
|
||||
<P><B>Description:</B>
|
||||
</P>
|
||||
|
|
@ -526,7 +522,7 @@ box size stored with the snapshot.
|
|||
</P>
|
||||
<UL><LI>acolor = * red/green/blue/yellow/aqua/cyan
|
||||
<LI>adiam = * 1.0
|
||||
<LI>amap = min max cf 2 0.0 blue 1.0 red
|
||||
<LI>amap = min max cf 2 min blue max red
|
||||
<LI>append = no
|
||||
<LI>bcolor = * red/green/blue/yellow/aqua/cyan
|
||||
<LI>bdiam = * 0.5
|
||||
|
|
|
|||
|
|
@ -8,10 +8,6 @@
|
|||
|
||||
dump_modify command :h3
|
||||
|
||||
NOTE: The keywords below which are only relevant for the "dump
|
||||
image"_dump_image.html command have not yet been released as part of
|
||||
LAMMPS.
|
||||
|
||||
[Syntax:]
|
||||
|
||||
dump_modify dump-ID keyword values ... :pre
|
||||
|
|
@ -95,8 +91,7 @@ dump_modify 1 region mySphere thresh x < 0.0 thresh epair >= 3.2
|
|||
dump_modify xtcdump precision 10000
|
||||
dump_modify 1 every 1000
|
||||
dump_modify 1 every v_myVar :pre
|
||||
|
||||
NOTE: need to add some image examples :pre
|
||||
dump_modify 1 amap min max cf 0.0 3 min green 0.5 yellow max blue boxcolor red :pre
|
||||
|
||||
[Description:]
|
||||
|
||||
|
|
@ -519,7 +514,7 @@ The option defaults are
|
|||
|
||||
acolor = * red/green/blue/yellow/aqua/cyan
|
||||
adiam = * 1.0
|
||||
amap = min max cf 2 0.0 blue 1.0 red
|
||||
amap = min max cf 2 min blue max red
|
||||
append = no
|
||||
bcolor = * red/green/blue/yellow/aqua/cyan
|
||||
bdiam = * 0.5
|
||||
|
|
|
|||
|
|
@ -0,0 +1,156 @@
|
|||
<HTML>
|
||||
<CENTER><A HREF = "http://lammps.sandia.gov">LAMMPS WWW Site</A> - <A HREF = "Manual.html">LAMMPS Documentation</A> - <A HREF = "Section_commands.html#comm">LAMMPS Commands</A>
|
||||
</CENTER>
|
||||
|
||||
|
||||
|
||||
|
||||
|
||||
|
||||
<HR>
|
||||
|
||||
<H3>pair_style adp command
|
||||
</H3>
|
||||
<P><B>Syntax:</B>
|
||||
</P>
|
||||
<PRE>pair_style adp
|
||||
</PRE>
|
||||
<P><B>Examples:</B>
|
||||
</P>
|
||||
<PRE>pair_style adp
|
||||
pair_coeff * * Ta.adp Ta
|
||||
pair_coeff * * ../potentials/AlCu.adp Al Al Cu
|
||||
</PRE>
|
||||
<P><B>Description:</B>
|
||||
</P>
|
||||
<P>Style <I>adp</I> computes pairwise interactions for metals and metal alloys
|
||||
using the angular dependent potential (ADP) of <A HREF = "#Mishin">(Mishin)</A>,
|
||||
which is a generalization of the <A HREF = "pair_eam.html">embedded atom method (EAM)
|
||||
potential</A>. The total energy Ei of an atom I is given
|
||||
by
|
||||
</P>
|
||||
<CENTER><IMG SRC = "Eqs/pair_adp.jpg">
|
||||
</CENTER>
|
||||
<P>where F is the embedding energy which is a function of the atomic
|
||||
electron density rho, phi is a pair potential interaction, alpha and
|
||||
beta are the element types of atoms I and J, and s and t = 1,2,3 and
|
||||
refer to the cartesian coordinates. The mu and lambda terms represent
|
||||
the dipole and quadruple distortions of the local atomic environment
|
||||
which extend the original EAM framework by introducing angular forces.
|
||||
</P>
|
||||
<P>Note that unlike for other potentials, cutoffs for ADP potentials are
|
||||
not set in the pair_style or pair_coeff command; they are specified in
|
||||
the ADP potential files themselves. Likewise, the ADP potential files
|
||||
list atomic masses; thus you do not need to use the <A HREF = "mass.html">mass</A>
|
||||
command to specify them.
|
||||
</P>
|
||||
<P>The NIST WWW site distributes and documents ADP potentials:
|
||||
</P>
|
||||
<PRE>http://www.ctcms.nist.gov/potentials
|
||||
</PRE>
|
||||
<P>Note that these must be converted into the extended DYNAMO <I>setfl</I>
|
||||
format discussed below.
|
||||
</P>
|
||||
<P>The NIST site is maintained by Chandler Becker (cbecker at nist.gov)
|
||||
who is good resource for info on interatomic potentials and file
|
||||
formats.
|
||||
</P>
|
||||
<HR>
|
||||
|
||||
<P>Only a single pair_coeff command is used with the <I>adp</I> style which
|
||||
specifies an extended DYNAMO <I>setfl</I> file, which contains information
|
||||
for M elements. These are mapped to LAMMPS atom types by specifying N
|
||||
additional arguments after the filename in the pair_coeff command,
|
||||
where N is the number of LAMMPS atom types:
|
||||
</P>
|
||||
<UL><LI>filename
|
||||
<LI>N element names = mapping of extended <I>setfl</I> elements to atom types
|
||||
</UL>
|
||||
<P>As an example, the potentials/AlCu.adp file is an extended <I>setfl</I>
|
||||
file which has tabulated ADP values for w elements and their alloy
|
||||
interactions: Cu and Al. If your LAMMPS simulation has 4 atoms types
|
||||
and you want the 1st 3 to be Al, and the 4th to be Cu, you would use
|
||||
the following pair_coeff command:
|
||||
</P>
|
||||
<PRE>pair_coeff * * AlCu.adp Al Al Al Cu
|
||||
</PRE>
|
||||
<P>The 1st 2 arguments must be * * so as to span all LAMMPS atom types.
|
||||
The first three Al arguments map LAMMPS atom types 1,2,3 to the Al
|
||||
element in the extended <I>setfl</I> file. The final Cu argument maps
|
||||
LAMMPS atom type 4 to the Al element in the extended <I>setfl</I> file.
|
||||
Note that there is no requirement that your simulation use all the
|
||||
elements specified by the extended <I>setfl</I> file.
|
||||
</P>
|
||||
<P>If a mapping value is specified as NULL, the mapping is not performed.
|
||||
This can be used when an <I>adp</I> potential is used as part of the
|
||||
<I>hybrid</I> pair style. The NULL values are placeholders for atom types
|
||||
that will be used with other potentials.
|
||||
</P>
|
||||
<P><I>Adp</I> files in the <I>potentials</I> directory of the LAMMPS distribution
|
||||
have an ".adp" suffix. A DYNAMO <I>setfl</I> file extended for ADP is
|
||||
formatted as follows. Basically it is the standard <I>setfl</I> format
|
||||
with additional tabulated functions u and w added to the file after
|
||||
the tabulated pair potentials. See the <A HREF = "pair_eam.html">pair_eam</A>
|
||||
command for further details on the <I>setfl</I> format.
|
||||
</P>
|
||||
<UL><LI>lines 1,2,3 = comments (ignored)
|
||||
<LI>line 4: Nelements Element1 Element2 ... ElementN
|
||||
<LI>line 5: Nrho, drho, Nr, dr, cutoff
|
||||
</UL>
|
||||
<P>Following the 5 header lines are Nelements sections, one for each
|
||||
element, each with the following format:
|
||||
</P>
|
||||
<UL><LI>line 1 = atomic number, mass, lattice constant, lattice type (e.g. FCC)
|
||||
<LI>embedding function F(rho) (Nrho values)
|
||||
<LI>density function rho(r) (Nr values)
|
||||
</UL>
|
||||
<P>Following the Nelements sections, Nr values for each pair potential
|
||||
phi(r) array are listed for all i,j element pairs in the same format
|
||||
as other arrays. Since these interactions are symmetric (i,j = j,i)
|
||||
only phi arrays with i >= j are listed, in the following order: i,j =
|
||||
(1,1), (2,1), (2,2), (3,1), (3,2), (3,3), (4,1), ..., (Nelements,
|
||||
Nelements).
|
||||
</P>
|
||||
<P>After the phi(r) arrays, each of the u(r) arrays are listed in the
|
||||
same order with the same assumptions of symmetry. Directly following
|
||||
the u(r), the w(r) arrays are listed.
|
||||
</P>
|
||||
<HR>
|
||||
|
||||
<P><B>Mixing, shift, table, tail correction, restart, rRESPA info</B>:
|
||||
</P>
|
||||
<P>For atom type pairs I,J and I != J, where types I and J correspond to
|
||||
two different element types, no special mixing rules are needed, since
|
||||
the ADP potential files specify alloy interactions explicitly.
|
||||
</P>
|
||||
<P>This pair style does not support the <A HREF = "pair_modify.html">pair_modify</A>
|
||||
shift, table, and tail options.
|
||||
</P>
|
||||
<P>This pair style does not write its information to <A HREF = "restart.html">binary restart
|
||||
files</A>, since it is stored in tabulated potential files.
|
||||
Thus, you need to re-specify the pair_style and pair_coeff commands in
|
||||
an input script that reads a restart file.
|
||||
</P>
|
||||
<P>This pair style can only be used via the <I>pair</I> keyword of the
|
||||
<A HREF = "run_style.html">run_style respa</A> command. It does not support the
|
||||
<I>inner</I>, <I>middle</I>, <I>outer</I> keywords.
|
||||
</P>
|
||||
<HR>
|
||||
|
||||
<P><B>Restrictions:</B>
|
||||
</P>
|
||||
<P>This pair style is part of the "manybody" package. It is only enabled
|
||||
if LAMMPS was built with that package (which it is by default).
|
||||
</P>
|
||||
<P><B>Related commands:</B>
|
||||
</P>
|
||||
<P><A HREF = "pair_coeff.html">pair_coeff</A>, <A HREF = "pair_eam.html">pair_eam</A>
|
||||
</P>
|
||||
<P><B>Default:</B> none
|
||||
</P>
|
||||
<HR>
|
||||
|
||||
<P>:link(Mishin) <B>(Mishin)</B> Mishin, Mehl, and Papaconstantopoulos, Acta
|
||||
Mater, 53, 4029 (2005).
|
||||
</P>
|
||||
</HTML>
|
||||
|
|
@ -0,0 +1,151 @@
|
|||
"LAMMPS WWW Site"_lws - "LAMMPS Documentation"_ld - "LAMMPS Commands"_lc :c
|
||||
|
||||
:link(lws,http://lammps.sandia.gov)
|
||||
:link(ld,Manual.html)
|
||||
:link(lc,Section_commands.html#comm)
|
||||
|
||||
:line
|
||||
|
||||
pair_style adp command :h3
|
||||
|
||||
[Syntax:]
|
||||
|
||||
pair_style adp :pre
|
||||
|
||||
[Examples:]
|
||||
|
||||
pair_style adp
|
||||
pair_coeff * * Ta.adp Ta
|
||||
pair_coeff * * ../potentials/AlCu.adp Al Al Cu :pre
|
||||
|
||||
[Description:]
|
||||
|
||||
Style {adp} computes pairwise interactions for metals and metal alloys
|
||||
using the angular dependent potential (ADP) of "(Mishin)"_#Mishin,
|
||||
which is a generalization of the "embedded atom method (EAM)
|
||||
potential"_pair_eam.html. The total energy Ei of an atom I is given
|
||||
by
|
||||
|
||||
:c,image(Eqs/pair_adp.jpg)
|
||||
|
||||
where F is the embedding energy which is a function of the atomic
|
||||
electron density rho, phi is a pair potential interaction, alpha and
|
||||
beta are the element types of atoms I and J, and s and t = 1,2,3 and
|
||||
refer to the cartesian coordinates. The mu and lambda terms represent
|
||||
the dipole and quadruple distortions of the local atomic environment
|
||||
which extend the original EAM framework by introducing angular forces.
|
||||
|
||||
Note that unlike for other potentials, cutoffs for ADP potentials are
|
||||
not set in the pair_style or pair_coeff command; they are specified in
|
||||
the ADP potential files themselves. Likewise, the ADP potential files
|
||||
list atomic masses; thus you do not need to use the "mass"_mass.html
|
||||
command to specify them.
|
||||
|
||||
The NIST WWW site distributes and documents ADP potentials:
|
||||
|
||||
http://www.ctcms.nist.gov/potentials :pre
|
||||
|
||||
Note that these must be converted into the extended DYNAMO {setfl}
|
||||
format discussed below.
|
||||
|
||||
The NIST site is maintained by Chandler Becker (cbecker at nist.gov)
|
||||
who is good resource for info on interatomic potentials and file
|
||||
formats.
|
||||
|
||||
:line
|
||||
|
||||
Only a single pair_coeff command is used with the {adp} style which
|
||||
specifies an extended DYNAMO {setfl} file, which contains information
|
||||
for M elements. These are mapped to LAMMPS atom types by specifying N
|
||||
additional arguments after the filename in the pair_coeff command,
|
||||
where N is the number of LAMMPS atom types:
|
||||
|
||||
filename
|
||||
N element names = mapping of extended {setfl} elements to atom types :ul
|
||||
|
||||
As an example, the potentials/AlCu.adp file is an extended {setfl}
|
||||
file which has tabulated ADP values for w elements and their alloy
|
||||
interactions: Cu and Al. If your LAMMPS simulation has 4 atoms types
|
||||
and you want the 1st 3 to be Al, and the 4th to be Cu, you would use
|
||||
the following pair_coeff command:
|
||||
|
||||
pair_coeff * * AlCu.adp Al Al Al Cu :pre
|
||||
|
||||
The 1st 2 arguments must be * * so as to span all LAMMPS atom types.
|
||||
The first three Al arguments map LAMMPS atom types 1,2,3 to the Al
|
||||
element in the extended {setfl} file. The final Cu argument maps
|
||||
LAMMPS atom type 4 to the Al element in the extended {setfl} file.
|
||||
Note that there is no requirement that your simulation use all the
|
||||
elements specified by the extended {setfl} file.
|
||||
|
||||
If a mapping value is specified as NULL, the mapping is not performed.
|
||||
This can be used when an {adp} potential is used as part of the
|
||||
{hybrid} pair style. The NULL values are placeholders for atom types
|
||||
that will be used with other potentials.
|
||||
|
||||
{Adp} files in the {potentials} directory of the LAMMPS distribution
|
||||
have an ".adp" suffix. A DYNAMO {setfl} file extended for ADP is
|
||||
formatted as follows. Basically it is the standard {setfl} format
|
||||
with additional tabulated functions u and w added to the file after
|
||||
the tabulated pair potentials. See the "pair_eam"_pair_eam.html
|
||||
command for further details on the {setfl} format.
|
||||
|
||||
lines 1,2,3 = comments (ignored)
|
||||
line 4: Nelements Element1 Element2 ... ElementN
|
||||
line 5: Nrho, drho, Nr, dr, cutoff :ul
|
||||
|
||||
Following the 5 header lines are Nelements sections, one for each
|
||||
element, each with the following format:
|
||||
|
||||
line 1 = atomic number, mass, lattice constant, lattice type (e.g. FCC)
|
||||
embedding function F(rho) (Nrho values)
|
||||
density function rho(r) (Nr values) :ul
|
||||
|
||||
Following the Nelements sections, Nr values for each pair potential
|
||||
phi(r) array are listed for all i,j element pairs in the same format
|
||||
as other arrays. Since these interactions are symmetric (i,j = j,i)
|
||||
only phi arrays with i >= j are listed, in the following order: i,j =
|
||||
(1,1), (2,1), (2,2), (3,1), (3,2), (3,3), (4,1), ..., (Nelements,
|
||||
Nelements).
|
||||
|
||||
After the phi(r) arrays, each of the u(r) arrays are listed in the
|
||||
same order with the same assumptions of symmetry. Directly following
|
||||
the u(r), the w(r) arrays are listed.
|
||||
|
||||
:line
|
||||
|
||||
[Mixing, shift, table, tail correction, restart, rRESPA info]:
|
||||
|
||||
For atom type pairs I,J and I != J, where types I and J correspond to
|
||||
two different element types, no special mixing rules are needed, since
|
||||
the ADP potential files specify alloy interactions explicitly.
|
||||
|
||||
This pair style does not support the "pair_modify"_pair_modify.html
|
||||
shift, table, and tail options.
|
||||
|
||||
This pair style does not write its information to "binary restart
|
||||
files"_restart.html, since it is stored in tabulated potential files.
|
||||
Thus, you need to re-specify the pair_style and pair_coeff commands in
|
||||
an input script that reads a restart file.
|
||||
|
||||
This pair style can only be used via the {pair} keyword of the
|
||||
"run_style respa"_run_style.html command. It does not support the
|
||||
{inner}, {middle}, {outer} keywords.
|
||||
|
||||
:line
|
||||
|
||||
[Restrictions:]
|
||||
|
||||
This pair style is part of the "manybody" package. It is only enabled
|
||||
if LAMMPS was built with that package (which it is by default).
|
||||
|
||||
[Related commands:]
|
||||
|
||||
"pair_coeff"_pair_coeff.html, "pair_eam"_pair_eam.html
|
||||
|
||||
[Default:] none
|
||||
|
||||
:line
|
||||
|
||||
:link(Mishin) [(Mishin)] Mishin, Mehl, and Papaconstantopoulos, Acta
|
||||
Mater, 53, 4029 (2005).
|
||||
|
|
@ -122,19 +122,19 @@ the pair_style command.
|
|||
</P>
|
||||
<HR>
|
||||
|
||||
<P>The <I>lj/charmm/coul/long/opt</I> style is identical to the
|
||||
<I>lj/charmm/coul/long</I> style, except that it is written in an optimized
|
||||
<P>The styles with an <I>opt</I> suffix are identical to the corresponding
|
||||
styles without the suffix, except that it is written in an optimized
|
||||
fashion for faster CPU execution. See <A HREF = "doc/Section_accerate.html">this
|
||||
section</A> of the manual for more details.
|
||||
</P>
|
||||
<P>The <I>lj/charmm/coul/long/gpu</I> style is identical to the
|
||||
<I>lj/charmm/coul/long</I> style, except that each processor off-loads its
|
||||
<P>The styles with a <I>gpu</I> suffix are identical to the corresponding
|
||||
styles without the suffix, except that each processor off-loads its
|
||||
pairwise calculations to a GPU. Depending on the hardware available
|
||||
on your system this can provide a significant speed-up. See <A HREF = "doc/Section_accerate.html">this
|
||||
on your system this can provide a speed-up. See <A HREF = "doc/Section_accerate.html">this
|
||||
section</A> of the manual for more details.
|
||||
</P>
|
||||
<P>Additional requirements in your input script to run with style
|
||||
<I>lj/charmm/coul/long/gpu</I> are as follows:
|
||||
<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
|
||||
|
|
@ -181,18 +181,11 @@ support the <I>pair</I> keyword of run_style respa. See the
|
|||
</P>
|
||||
<P>The <I>lj/charmm/coul/charmm</I> and <I>lj/charmm/coul/charmm/implicit</I>
|
||||
styles are part of the "molecule" package. The <I>lj/charmm/coul/long</I>
|
||||
style is part of the "kspace" package. The <I>lj/charmm/coul/long/gpu</I>
|
||||
style is part of the "gpu" package and also requires the "kspace"
|
||||
package. The <I>lj/charmm/coul/long/opt</I>
|
||||
style is part of the "opt" package and also requires the "kspace"
|
||||
package. They are only enabled if LAMMPS was built with those
|
||||
package(s) (molecule and kspace are by default). See the <A HREF = "Section_start.html#2_3">Making
|
||||
LAMMPS</A> section for more info.
|
||||
</P>
|
||||
<P>On some 64-bit machines, compiling with -O3 appears to break the
|
||||
Coulombic tabling option used by the <I>lj/charmm/coul/long</I> style. See
|
||||
the "Additional build tips" section of the Making LAMMPS documentation
|
||||
pages for workarounds on this issue.
|
||||
style is part of the "kspace" package. The styles with an <I>opt</I> or
|
||||
<I>gpu</I> suffix are part of the "opt" or "gpu" packages. They are only
|
||||
enabled if LAMMPS was built with those packages. See the <A HREF = "Section_start.html#2_3">Making
|
||||
LAMMPS</A> section for more info. Note that the
|
||||
molecule and kspace packages are installed by default.
|
||||
</P>
|
||||
<P><B>Related commands:</B>
|
||||
</P>
|
||||
|
|
|
|||
|
|
@ -114,19 +114,19 @@ the pair_style command.
|
|||
|
||||
:line
|
||||
|
||||
The {lj/charmm/coul/long/opt} style is identical to the
|
||||
{lj/charmm/coul/long} style, except that it is written in an optimized
|
||||
The styles with an {opt} suffix are identical to the corresponding
|
||||
styles without the suffix, except that it is written in an optimized
|
||||
fashion for faster CPU execution. See "this
|
||||
section"_doc/Section_accerate.html of the manual for more details.
|
||||
|
||||
The {lj/charmm/coul/long/gpu} style is identical to the
|
||||
{lj/charmm/coul/long} style, except that each processor off-loads its
|
||||
The styles with a {gpu} suffix are identical to the corresponding
|
||||
styles without the suffix, except that each processor off-loads its
|
||||
pairwise calculations to a GPU. Depending on the hardware available
|
||||
on your system this can provide a significant speed-up. See "this
|
||||
on your system this can provide a speed-up. See "this
|
||||
section"_doc/Section_accerate.html of the manual for more details.
|
||||
|
||||
Additional requirements in your input script to run with style
|
||||
{lj/charmm/coul/long/gpu} are as follows:
|
||||
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
|
||||
|
|
@ -173,18 +173,11 @@ support the {pair} keyword of run_style respa. See the
|
|||
|
||||
The {lj/charmm/coul/charmm} and {lj/charmm/coul/charmm/implicit}
|
||||
styles are part of the "molecule" package. The {lj/charmm/coul/long}
|
||||
style is part of the "kspace" package. The {lj/charmm/coul/long/gpu}
|
||||
style is part of the "gpu" package and also requires the "kspace"
|
||||
package. The {lj/charmm/coul/long/opt}
|
||||
style is part of the "opt" package and also requires the "kspace"
|
||||
package. They are only enabled if LAMMPS was built with those
|
||||
package(s) (molecule and kspace are by default). See the "Making
|
||||
LAMMPS"_Section_start.html#2_3 section for more info.
|
||||
|
||||
On some 64-bit machines, compiling with -O3 appears to break the
|
||||
Coulombic tabling option used by the {lj/charmm/coul/long} style. See
|
||||
the "Additional build tips" section of the Making LAMMPS documentation
|
||||
pages for workarounds on this issue.
|
||||
style is part of the "kspace" package. The styles with an {opt} or
|
||||
{gpu} suffix are part of the "opt" or "gpu" packages. They are only
|
||||
enabled if LAMMPS was built with those packages. See the "Making
|
||||
LAMMPS"_Section_start.html#2_3 section for more info. Note that the
|
||||
molecule and kspace packages are installed by default.
|
||||
|
||||
[Related commands:]
|
||||
|
||||
|
|
|
|||
|
|
@ -11,15 +11,19 @@
|
|||
|
||||
<H3>pair_style lj/class2 command
|
||||
</H3>
|
||||
<H3>pair_style lj/class2/gpu command
|
||||
</H3>
|
||||
<H3>pair_style lj/class2/coul/cut command
|
||||
</H3>
|
||||
<H3>pair_style lj/class2/coul/long command
|
||||
</H3>
|
||||
<H3>pair_style lj/class2/coul/long/gpu command
|
||||
</H3>
|
||||
<P><B>Syntax:</B>
|
||||
</P>
|
||||
<PRE>pair_style style args
|
||||
</PRE>
|
||||
<UL><LI>style = <I>lj/class2</I> or <I>lj/class2/coul/cut</I> or <I>lj/class2/coul/long</I>
|
||||
<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>
|
||||
<LI>args = list of arguments for a particular style
|
||||
</UL>
|
||||
<PRE> <I>lj/class2</I> args = cutoff
|
||||
|
|
@ -34,6 +38,7 @@
|
|||
<P><B>Examples:</B>
|
||||
</P>
|
||||
<PRE>pair_style lj/class2 10.0
|
||||
pair_style lj/class2/gpu 10.0
|
||||
pair_coeff * * 100.0 2.5
|
||||
pair_coeff 1 2* 100.0 2.5 9.0
|
||||
</PRE>
|
||||
|
|
@ -44,6 +49,7 @@ pair_coeff 1 1 100.0 3.5 9.0
|
|||
pair_coeff 1 1 100.0 3.5 9.0 9.0
|
||||
</PRE>
|
||||
<PRE>pair_style lj/class2/coul/long 10.0
|
||||
pair_style lj/class2/coul/long/gpu 10.0
|
||||
pair_style lj/class2/coul/long 10.0 8.0
|
||||
pair_coeff * * 100.0 3.0
|
||||
pair_coeff 1 1 100.0 3.5 9.0
|
||||
|
|
@ -56,10 +62,16 @@ pair_coeff 1 1 100.0 3.5 9.0
|
|||
</CENTER>
|
||||
<P>Rc is the cutoff.
|
||||
</P>
|
||||
<P>Style <I>lj/class2/gpu</I> is a GPU-enabled version of style <I>lj/class2</I>.
|
||||
See more details below.
|
||||
</P>
|
||||
<P>The <I>lj/class2/coul/cut</I> and <I>lj/class2/coul/long</I> styles add a
|
||||
Coulombic term as described for the <A HREF = "pair_lj.html">lj/cut</A> pair
|
||||
styles.
|
||||
</P>
|
||||
<P>Style <I>lj/class2/coul/long/gpu</I> is a GPU-enabled version of style
|
||||
<I>lj/class2/coul/long</I>. See more details below.
|
||||
</P>
|
||||
<P>See <A HREF = "#Sun">(Sun)</A> for a description of the COMPASS class2 force field.
|
||||
</P>
|
||||
<P>The following coefficients must be defined for each pair of atoms
|
||||
|
|
@ -96,6 +108,21 @@ mix</A> setting is thus ignored for class2 potentials
|
|||
for epsilon and sigma. However it is still followed for mixing the
|
||||
cutoff distance.
|
||||
</P>
|
||||
<HR>
|
||||
|
||||
<P>The styles with a <I>gpu</I> suffix are identical to the corresponding
|
||||
styles without the suffix, except that each processor off-loads its
|
||||
pairwise calculations to a GPU. Depending on the hardware available
|
||||
on your system this can provide a speed-up. See <A HREF = "doc/Section_accerate.html">this
|
||||
section</A> of the manual for more details.
|
||||
</P>
|
||||
<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><B>Mixing, shift, table, tail correction, restart, rRESPA info</B>:
|
||||
</P>
|
||||
<P>For atom type pairs I,J and I != J, the epsilon and sigma coefficients
|
||||
|
|
@ -128,9 +155,11 @@ support the <I>inner</I>, <I>middle</I>, <I>outer</I> keywords.
|
|||
</P>
|
||||
<P><B>Restrictions:</B>
|
||||
</P>
|
||||
<P>All of these pair styles are part of the "class2" package. They are
|
||||
only enabled if LAMMPS was built with that package. See the <A HREF = "Section_start.html#2_3">Making
|
||||
LAMMPS</A> section for more info.
|
||||
<P>All of these pair styles, except those ending in "gpu", are part of
|
||||
the "class2" package. They are only enabled if LAMMPS was built with
|
||||
that package. The styles with a <I>gpu</I> suffix are part of the "gpu"
|
||||
package. They are only enabled if LAMMPS was built with that package.
|
||||
See the <A HREF = "Section_start.html#2_3">Making LAMMPS</A> section for more info.
|
||||
</P>
|
||||
<P><B>Related commands:</B>
|
||||
</P>
|
||||
|
|
|
|||
|
|
@ -7,14 +7,16 @@
|
|||
:line
|
||||
|
||||
pair_style lj/class2 command :h3
|
||||
pair_style lj/class2/gpu command :h3
|
||||
pair_style lj/class2/coul/cut command :h3
|
||||
pair_style lj/class2/coul/long command :h3
|
||||
pair_style lj/class2/coul/long/gpu command :h3
|
||||
|
||||
[Syntax:]
|
||||
|
||||
pair_style style args :pre
|
||||
|
||||
style = {lj/class2} or {lj/class2/coul/cut} or {lj/class2/coul/long}
|
||||
style = {lj/class2} or {lj/class2/gpu} or {lj/class2/coul/cut} or {lj/class2/coul/long} or {lj/class2/coul/long/gpu}
|
||||
args = list of arguments for a particular style :ul
|
||||
{lj/class2} args = cutoff
|
||||
cutoff = global cutoff for class 2 interactions (distance units)
|
||||
|
|
@ -28,6 +30,7 @@ args = list of arguments for a particular style :ul
|
|||
[Examples:]
|
||||
|
||||
pair_style lj/class2 10.0
|
||||
pair_style lj/class2/gpu 10.0
|
||||
pair_coeff * * 100.0 2.5
|
||||
pair_coeff 1 2* 100.0 2.5 9.0 :pre
|
||||
|
||||
|
|
@ -38,6 +41,7 @@ pair_coeff 1 1 100.0 3.5 9.0
|
|||
pair_coeff 1 1 100.0 3.5 9.0 9.0 :pre
|
||||
|
||||
pair_style lj/class2/coul/long 10.0
|
||||
pair_style lj/class2/coul/long/gpu 10.0
|
||||
pair_style lj/class2/coul/long 10.0 8.0
|
||||
pair_coeff * * 100.0 3.0
|
||||
pair_coeff 1 1 100.0 3.5 9.0 :pre
|
||||
|
|
@ -50,10 +54,16 @@ The {lj/class2} styles compute a 6/9 Lennard-Jones potential given by
|
|||
|
||||
Rc is the cutoff.
|
||||
|
||||
Style {lj/class2/gpu} is a GPU-enabled version of style {lj/class2}.
|
||||
See more details below.
|
||||
|
||||
The {lj/class2/coul/cut} and {lj/class2/coul/long} styles add a
|
||||
Coulombic term as described for the "lj/cut"_pair_lj.html pair
|
||||
styles.
|
||||
|
||||
Style {lj/class2/coul/long/gpu} is a GPU-enabled version of style
|
||||
{lj/class2/coul/long}. See more details below.
|
||||
|
||||
See "(Sun)"_#Sun for a description of the COMPASS class2 force field.
|
||||
|
||||
The following coefficients must be defined for each pair of atoms
|
||||
|
|
@ -90,6 +100,21 @@ mix"_pair_modify.html setting is thus ignored for class2 potentials
|
|||
for epsilon and sigma. However it is still followed for mixing the
|
||||
cutoff distance.
|
||||
|
||||
:line
|
||||
|
||||
The styles with a {gpu} suffix are identical to the corresponding
|
||||
styles without the suffix, except that each processor off-loads its
|
||||
pairwise calculations to a GPU. Depending on the hardware available
|
||||
on your system this can provide a speed-up. See "this
|
||||
section"_doc/Section_accerate.html of the manual for more details.
|
||||
|
||||
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.
|
||||
|
||||
[Mixing, shift, table, tail correction, restart, rRESPA info]:
|
||||
|
||||
For atom type pairs I,J and I != J, the epsilon and sigma coefficients
|
||||
|
|
@ -122,9 +147,11 @@ support the {inner}, {middle}, {outer} keywords.
|
|||
|
||||
[Restrictions:]
|
||||
|
||||
All of these pair styles are part of the "class2" package. They are
|
||||
only enabled if LAMMPS was built with that package. See the "Making
|
||||
LAMMPS"_Section_start.html#2_3 section for more info.
|
||||
All of these pair styles, except those ending in "gpu", are part of
|
||||
the "class2" package. They are only enabled if LAMMPS was built with
|
||||
that package. The styles with a {gpu} suffix are part of the "gpu"
|
||||
package. They are only enabled if LAMMPS was built with that package.
|
||||
See the "Making LAMMPS"_Section_start.html#2_3 section for more info.
|
||||
|
||||
[Related commands:]
|
||||
|
||||
|
|
|
|||
|
|
@ -129,15 +129,14 @@ pair_style command.
|
|||
</P>
|
||||
<HR>
|
||||
|
||||
<P>The <I>cg/cmm/gpu</I> and <I>cg/cmm/coul/long/gpu</I> styles are identical to
|
||||
the <I>cg/cmm</I> and <I>cg/cmm/coul/long</I> styles, except that each processor
|
||||
off-loads its pairwise calculations to a GPU. Depending on the
|
||||
hardware available on your system this can provide a speed-up. See
|
||||
<A HREF = "doc/Section_accerate.html">this section</A> of the manual for more
|
||||
details.
|
||||
<P>The styles with a <I>gpu</I> suffix are identical to the corresponding
|
||||
styles without the suffix, except that each processor off-loads its
|
||||
pairwise calculations to a GPU. Depending on the hardware available
|
||||
on your system this can provide a speed-up. See <A HREF = "doc/Section_accerate.html">this
|
||||
section</A> of the manual for more details.
|
||||
</P>
|
||||
<P>Additional requirements in your input script to run with GPU-enabled
|
||||
styles are as follows:
|
||||
<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
|
||||
|
|
@ -177,16 +176,13 @@ See the <A HREF = "run_style.html">run_style</A> command for details.
|
|||
<P><B>Restrictions:</B>
|
||||
</P>
|
||||
<P>All of the cg/cmm pair styles are part of the "user-cg-cmm"
|
||||
package. They are only enabled if LAMMPS was built with that
|
||||
package. The <I>cg/cmm/coul/long</I> style also requires the "kspace"
|
||||
package to be built (which is enabled by default). See the <A HREF = "Section_start.html#2_3">Making
|
||||
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
|
||||
built (which is enabled by default). The styles with a <I>gpu</I> suffix
|
||||
are part of the "gpu" package. They are only enabled if LAMMPS was
|
||||
built with that package. See the <A HREF = "Section_start.html#2_3">Making
|
||||
LAMMPS</A> section for more info.
|
||||
</P>
|
||||
<P>On some 64-bit machines, compiling with -O3 appears to break the
|
||||
Coulombic tabling option used by the <I>cg/cmm/coul/long</I> style. See
|
||||
the "Additional build tips" section of the Making LAMMPS documentation
|
||||
pages for workarounds on this issue.
|
||||
</P>
|
||||
<P><B>Related commands:</B>
|
||||
</P>
|
||||
<P><A HREF = "pair_coeff.html">pair_coeff</A>, <A HREF = "angle_cmm.html">angle_style cg/cmm</A>
|
||||
|
|
|
|||
|
|
@ -120,15 +120,14 @@ pair_style command.
|
|||
|
||||
:line
|
||||
|
||||
The {cg/cmm/gpu} and {cg/cmm/coul/long/gpu} styles are identical to
|
||||
the {cg/cmm} and {cg/cmm/coul/long} styles, except that each processor
|
||||
off-loads its pairwise calculations to a GPU. Depending on the
|
||||
hardware available on your system this can provide a speed-up. See
|
||||
"this section"_doc/Section_accerate.html of the manual for more
|
||||
details.
|
||||
The styles with a {gpu} suffix are identical to the corresponding
|
||||
styles without the suffix, except that each processor off-loads its
|
||||
pairwise calculations to a GPU. Depending on the hardware available
|
||||
on your system this can provide a speed-up. See "this
|
||||
section"_doc/Section_accerate.html of the manual for more details.
|
||||
|
||||
Additional requirements in your input script to run with GPU-enabled
|
||||
styles are as follows:
|
||||
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
|
||||
|
|
@ -168,16 +167,13 @@ See the "run_style"_run_style.html command for details.
|
|||
[Restrictions:]
|
||||
|
||||
All of the cg/cmm pair styles are part of the "user-cg-cmm"
|
||||
package. They are only enabled if LAMMPS was built with that
|
||||
package. The {cg/cmm/coul/long} style also requires the "kspace"
|
||||
package to be built (which is enabled by default). See the "Making
|
||||
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
|
||||
built (which is enabled by default). The styles with a {gpu} suffix
|
||||
are part of the "gpu" package. They are only enabled if LAMMPS was
|
||||
built with that package. See the "Making
|
||||
LAMMPS"_Section_start.html#2_3 section for more info.
|
||||
|
||||
On some 64-bit machines, compiling with -O3 appears to break the
|
||||
Coulombic tabling option used by the {cg/cmm/coul/long} style. See
|
||||
the "Additional build tips" section of the Making LAMMPS documentation
|
||||
pages for workarounds on this issue.
|
||||
|
||||
[Related commands:]
|
||||
|
||||
"pair_coeff"_pair_coeff.html, "angle_style cg/cmm"_angle_cmm.html
|
||||
|
|
|
|||
|
|
@ -87,7 +87,8 @@ the pair_style command, and coefficients specified by the associated
|
|||
<UL><LI><A HREF = "pair_hybrid.html">pair_style hybrid</A> - multiple styles of pairwise interactions
|
||||
<LI><A HREF = "pair_hybrid.html">pair_style hybrid/overlay</A> - multiple styles of superposed pairwise interactions
|
||||
</UL>
|
||||
<UL><LI><A HREF = "pair_airebo.html">pair_style airebo</A> - AIREBO potential of Stuart
|
||||
<UL><LI><A HREF = "pair_adp.html">pair_style adp</A> - angular dependent potential (ADP) of Mishin
|
||||
<LI><A HREF = "pair_airebo.html">pair_style airebo</A> - AIREBO potential of Stuart
|
||||
<LI><A HREF = "pair_born.html">pair_style born</A> - Born-Mayer-Huggins potential
|
||||
<LI><A HREF = "pair_born.html">pair_style born/coul/long</A> - Born-Mayer-Huggins with long-range Coulomb
|
||||
<LI><A HREF = "pair_buck.html">pair_style buck</A> - Buckingham potential
|
||||
|
|
|
|||
|
|
@ -84,6 +84,7 @@ the pair_style command, and coefficients specified by the associated
|
|||
"pair_style hybrid"_pair_hybrid.html - multiple styles of pairwise interactions
|
||||
"pair_style hybrid/overlay"_pair_hybrid.html - multiple styles of superposed pairwise interactions :ul
|
||||
|
||||
"pair_style adp"_pair_adp.html - angular dependent potential (ADP) of Mishin
|
||||
"pair_style airebo"_pair_airebo.html - AIREBO potential of Stuart
|
||||
"pair_style born"_pair_born.html - Born-Mayer-Huggins potential
|
||||
"pair_style born/coul/long"_pair_born.html - Born-Mayer-Huggins with long-range Coulomb
|
||||
|
|
|
|||
|
|
@ -123,11 +123,6 @@ enabled if LAMMPS was built with that package (which it is by
|
|||
default). See the <A HREF = "Section_start.html#2_3">Making LAMMPS</A> section for
|
||||
more info.
|
||||
</P>
|
||||
<P>On some 64-bit machines, compiling with -O3 appears to break the
|
||||
Coulombic tabling option used by the <I>coul/long</I> style. See the
|
||||
"Additional build tips" section of the Making LAMMPS documentation
|
||||
pages for workarounds on this issue.
|
||||
</P>
|
||||
<P><B>Related commands:</B>
|
||||
</P>
|
||||
<P><A HREF = "pair_coeff.html">pair_coeff</A>, <A HREF = "pair_hybrid.html">pair_style
|
||||
|
|
|
|||
|
|
@ -118,11 +118,6 @@ enabled if LAMMPS was built with that package (which it is by
|
|||
default). See the "Making LAMMPS"_Section_start.html#2_3 section for
|
||||
more info.
|
||||
|
||||
On some 64-bit machines, compiling with -O3 appears to break the
|
||||
Coulombic tabling option used by the {coul/long} style. See the
|
||||
"Additional build tips" section of the Making LAMMPS documentation
|
||||
pages for workarounds on this issue.
|
||||
|
||||
[Related commands:]
|
||||
|
||||
"pair_coeff"_pair_coeff.html, "pair_style
|
||||
|
|
|
|||
|
|
@ -38,14 +38,14 @@ pair_coeff 1*3 1*3 niu3.eam
|
|||
</PRE>
|
||||
<PRE>pair_style eam/alloy
|
||||
pair_style eam/alloy/opt
|
||||
pair_coeff * * ../potentials/nialhjea.eam.alloy Ni Al Ni Ni
|
||||
pair_coeff * * ../potentials/NiAlH_jea.eam.alloy Ni Al Ni Ni
|
||||
</PRE>
|
||||
<PRE>pair_style eam/cd
|
||||
pair_coeff * * ../potentials/FeCr.cdeam Fe Cr
|
||||
</PRE>
|
||||
<PRE>pair_style eam/fs
|
||||
pair_style eam/fs/opt
|
||||
pair_coeff * * nialhjea.eam.fs Ni Al Ni Ni
|
||||
pair_coeff * * NiAlH_jea.eam.fs Ni Al Ni Ni
|
||||
</PRE>
|
||||
<P><B>Description:</B>
|
||||
</P>
|
||||
|
|
@ -202,13 +202,13 @@ where N is the number of LAMMPS atom types:
|
|||
<UL><LI>filename
|
||||
<LI>N element names = mapping of <I>setfl</I> elements to atom types
|
||||
</UL>
|
||||
<P>As an example, the potentials/nialhjea <I>setfl</I> file has tabulated EAM
|
||||
values for 3 elements and their alloy interactions: Ni, Al, and H. If
|
||||
your LAMMPS simulation has 4 atoms types and you want the 1st 3 to be
|
||||
Ni, and the 4th to be Al, you would use the following pair_coeff
|
||||
command:
|
||||
<P>As an example, the potentials/NiAlH_jea.eam.alloy file is a <I>setfl</I>
|
||||
file which has tabulated EAM values for 3 elements and their alloy
|
||||
interactions: Ni, Al, and H. If your LAMMPS simulation has 4 atoms
|
||||
types and you want the 1st 3 to be Ni, and the 4th to be Al, you would
|
||||
use the following pair_coeff command:
|
||||
</P>
|
||||
<PRE>pair_coeff * * nialhjea.eam.alloy Ni Ni Ni Al
|
||||
<PRE>pair_coeff * * NiAlH_jea.eam.alloy Ni Ni Ni Al
|
||||
</PRE>
|
||||
<P>The 1st 2 arguments must be * * so as to span all LAMMPS atom types.
|
||||
The first three Ni arguments map LAMMPS atom types 1,2,3 to the Ni
|
||||
|
|
@ -323,7 +323,7 @@ FS potential files.
|
|||
<P>For style <I>eam/fs</I>, the form of the pair_coeff command is exactly the
|
||||
same as for style <I>eam/alloy</I>, e.g.
|
||||
</P>
|
||||
<PRE>pair_coeff * * nialhjea.eam.fs Ni Ni Ni Al
|
||||
<PRE>pair_coeff * * NiAlH_jea.eam.fs Ni Ni Ni Al
|
||||
</PRE>
|
||||
<P>where there are N additional arguments after the filename, where N is
|
||||
the number of LAMMPS atom types. The N values determine the mapping
|
||||
|
|
@ -371,9 +371,9 @@ are listed.
|
|||
</P>
|
||||
<HR>
|
||||
|
||||
<P>The <I>eam/opt</I>, <I>eam/alloy/opt</I>, and <I>eam/fs/opt</I> styles are identical
|
||||
to the <I>eam</I>, <I>eam/alloy</I>, and <I>eam/fs</I> styles, except that they are
|
||||
written in an optimized fashion for faster CPU execution. See <A HREF = "doc/Section_accerate.html">this
|
||||
<P>The styles with an <I>opt</I> suffix are identical to the corresponding
|
||||
styles without the suffix, except that it is written in an optimized
|
||||
fashion for faster CPU execution. See <A HREF = "doc/Section_accerate.html">this
|
||||
section</A> of the manual for more details.
|
||||
</P>
|
||||
<HR>
|
||||
|
|
@ -403,11 +403,9 @@ an input script that reads a restart file.
|
|||
</P>
|
||||
<P>All of these styles except those ending in <I>opt</I> and the <I>eam/cd</I>
|
||||
style are part of the "manybody" package. They are only enabled if
|
||||
LAMMPS was built with that package (which it is by default).
|
||||
</P>
|
||||
<P>The styles ending in <I>opt</I> are part of the "opt" package and also
|
||||
require the "manybody" package. They are only enabled if LAMMPS was
|
||||
built with those packages. See the <A HREF = "Section_start.html#2_3">Making
|
||||
LAMMPS was built with that package (which it is by default). The
|
||||
styles with an <I>opt</I> suffix are part of the "opt" package. They are
|
||||
only enabled if LAMMPS was built with that packages. See the <A HREF = "Section_start.html#2_3">Making
|
||||
LAMMPS</A> section for more info.
|
||||
</P>
|
||||
<P>The <I>eam/cd</I> style is part of the "user-cd-eam" package and also
|
||||
|
|
|
|||
|
|
@ -29,14 +29,14 @@ pair_coeff 1*3 1*3 niu3.eam :pre
|
|||
|
||||
pair_style eam/alloy
|
||||
pair_style eam/alloy/opt
|
||||
pair_coeff * * ../potentials/nialhjea.eam.alloy Ni Al Ni Ni :pre
|
||||
pair_coeff * * ../potentials/NiAlH_jea.eam.alloy Ni Al Ni Ni :pre
|
||||
|
||||
pair_style eam/cd
|
||||
pair_coeff * * ../potentials/FeCr.cdeam Fe Cr :pre
|
||||
|
||||
pair_style eam/fs
|
||||
pair_style eam/fs/opt
|
||||
pair_coeff * * nialhjea.eam.fs Ni Al Ni Ni :pre
|
||||
pair_coeff * * NiAlH_jea.eam.fs Ni Al Ni Ni :pre
|
||||
|
||||
[Description:]
|
||||
|
||||
|
|
@ -193,13 +193,13 @@ where N is the number of LAMMPS atom types:
|
|||
filename
|
||||
N element names = mapping of {setfl} elements to atom types :ul
|
||||
|
||||
As an example, the potentials/nialhjea {setfl} file has tabulated EAM
|
||||
values for 3 elements and their alloy interactions: Ni, Al, and H. If
|
||||
your LAMMPS simulation has 4 atoms types and you want the 1st 3 to be
|
||||
Ni, and the 4th to be Al, you would use the following pair_coeff
|
||||
command:
|
||||
As an example, the potentials/NiAlH_jea.eam.alloy file is a {setfl}
|
||||
file which has tabulated EAM values for 3 elements and their alloy
|
||||
interactions: Ni, Al, and H. If your LAMMPS simulation has 4 atoms
|
||||
types and you want the 1st 3 to be Ni, and the 4th to be Al, you would
|
||||
use the following pair_coeff command:
|
||||
|
||||
pair_coeff * * nialhjea.eam.alloy Ni Ni Ni Al :pre
|
||||
pair_coeff * * NiAlH_jea.eam.alloy Ni Ni Ni Al :pre
|
||||
|
||||
The 1st 2 arguments must be * * so as to span all LAMMPS atom types.
|
||||
The first three Ni arguments map LAMMPS atom types 1,2,3 to the Ni
|
||||
|
|
@ -314,7 +314,7 @@ FS potential files.
|
|||
For style {eam/fs}, the form of the pair_coeff command is exactly the
|
||||
same as for style {eam/alloy}, e.g.
|
||||
|
||||
pair_coeff * * nialhjea.eam.fs Ni Ni Ni Al :pre
|
||||
pair_coeff * * NiAlH_jea.eam.fs Ni Ni Ni Al :pre
|
||||
|
||||
where there are N additional arguments after the filename, where N is
|
||||
the number of LAMMPS atom types. The N values determine the mapping
|
||||
|
|
@ -362,9 +362,9 @@ are listed.
|
|||
|
||||
:line
|
||||
|
||||
The {eam/opt}, {eam/alloy/opt}, and {eam/fs/opt} styles are identical
|
||||
to the {eam}, {eam/alloy}, and {eam/fs} styles, except that they are
|
||||
written in an optimized fashion for faster CPU execution. See "this
|
||||
The styles with an {opt} suffix are identical to the corresponding
|
||||
styles without the suffix, except that it is written in an optimized
|
||||
fashion for faster CPU execution. See "this
|
||||
section"_doc/Section_accerate.html of the manual for more details.
|
||||
|
||||
:line
|
||||
|
|
@ -394,11 +394,9 @@ The eam pair styles can only be used via the {pair} keyword of the
|
|||
|
||||
All of these styles except those ending in {opt} and the {eam/cd}
|
||||
style are part of the "manybody" package. They are only enabled if
|
||||
LAMMPS was built with that package (which it is by default).
|
||||
|
||||
The styles ending in {opt} are part of the "opt" package and also
|
||||
require the "manybody" package. They are only enabled if LAMMPS was
|
||||
built with those packages. See the "Making
|
||||
LAMMPS was built with that package (which it is by default). The
|
||||
styles with an {opt} suffix are part of the "opt" package. They are
|
||||
only enabled if LAMMPS was built with that packages. See the "Making
|
||||
LAMMPS"_Section_start.html#2_3 section for more info.
|
||||
|
||||
The {eam/cd} style is part of the "user-cd-eam" package and also
|
||||
|
|
|
|||
|
|
@ -139,15 +139,14 @@ pair_coeff sigma to 1.0 as well.
|
|||
</P>
|
||||
<HR>
|
||||
|
||||
<P>The <I>gayberne/gpu</I> style is identical to the <I>gayberne</I> style, except
|
||||
that each processor off-loads its pairwise calculations to a GPU.
|
||||
Depending on the hardware available on your system this can provide a
|
||||
significant speed-up, especially for the relatively expensive
|
||||
computations inherent in Gay-Berne interactions. See <A HREF = "doc/Section_accerate.html">this
|
||||
<P>The styles with a <I>gpu</I> suffix are identical to the corresponding
|
||||
styles without the suffix, except that each processor off-loads its
|
||||
pairwise calculations to a GPU. Depending on the hardware available
|
||||
on your system this can provide a speed-up. See <A HREF = "doc/Section_accerate.html">this
|
||||
section</A> of the manual for more details.
|
||||
</P>
|
||||
<P>Additional requirements in your input script to run with style
|
||||
<I>gayberne/gpu</I> are as follows:
|
||||
<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
|
||||
|
|
@ -186,9 +185,9 @@ to be specified in an input script that reads a restart file.
|
|||
|
||||
<P><B>Restrictions:</B>
|
||||
</P>
|
||||
<P>The <I>gayberne</I> style is part of the "asphere" package. The
|
||||
<I>gayberne/gpu</I> style is part of the "gpu" package. They are only
|
||||
enabled if LAMMPS was built with the those packages. See the <A HREF = "Section_start.html#2_3">Making
|
||||
<P>The <I>gayberne</I> style is part of the "asphere" package. The styles
|
||||
with a <I>gpu</I> suffix are part of the "gpu" package. They are only
|
||||
enabled if LAMMPS was built with those packages. See the <A HREF = "Section_start.html#2_3">Making
|
||||
LAMMPS</A> section for more info.
|
||||
</P>
|
||||
<P>These pair style require that atoms store torque and a quaternion to
|
||||
|
|
|
|||
|
|
@ -134,15 +134,14 @@ pair_coeff sigma to 1.0 as well.
|
|||
|
||||
:line
|
||||
|
||||
The {gayberne/gpu} style is identical to the {gayberne} style, except
|
||||
that each processor off-loads its pairwise calculations to a GPU.
|
||||
Depending on the hardware available on your system this can provide a
|
||||
significant speed-up, especially for the relatively expensive
|
||||
computations inherent in Gay-Berne interactions. See "this
|
||||
The styles with a {gpu} suffix are identical to the corresponding
|
||||
styles without the suffix, except that each processor off-loads its
|
||||
pairwise calculations to a GPU. Depending on the hardware available
|
||||
on your system this can provide a speed-up. See "this
|
||||
section"_doc/Section_accerate.html of the manual for more details.
|
||||
|
||||
Additional requirements in your input script to run with style
|
||||
{gayberne/gpu} are as follows:
|
||||
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
|
||||
|
|
@ -181,9 +180,9 @@ This pair style can only be used via the {pair} keyword of the
|
|||
|
||||
[Restrictions:]
|
||||
|
||||
The {gayberne} style is part of the "asphere" package. The
|
||||
{gayberne/gpu} style is part of the "gpu" package. They are only
|
||||
enabled if LAMMPS was built with the those packages. See the "Making
|
||||
The {gayberne} style is part of the "asphere" package. The styles
|
||||
with a {gpu} suffix are part of the "gpu" package. They are only
|
||||
enabled if LAMMPS was built with those packages. See the "Making
|
||||
LAMMPS"_Section_start.html#2_3 section for more info.
|
||||
|
||||
These pair style require that atoms store torque and a quaternion to
|
||||
|
|
|
|||
|
|
@ -189,20 +189,19 @@ Coulombic cutoff specified in the pair_style command.
|
|||
</P>
|
||||
<HR>
|
||||
|
||||
<P>The <I>lj/cut/opt</I> style is identical to the <I>lj/cut</I> style, except that
|
||||
it is written in an optimized fashion for faster CPU execution. See
|
||||
<A HREF = "doc/Section_accerate.html">this section</A> of the manual for more
|
||||
details.
|
||||
<P>The styles with an <I>opt</I> suffix are identical to the corresponding
|
||||
styles without the suffix, except that it is written in an optimized
|
||||
fashion for faster CPU execution. See <A HREF = "doc/Section_accerate.html">this
|
||||
section</A> of the manual for more details.
|
||||
</P>
|
||||
<P>The <I>lj/cut/gpu</I>, <I>lj/cut/coul/cut/gpu</I>, and <I>lj/cut/coul/long/gpu</I>
|
||||
styles are identical to the <I>lj/cut</I>, <I>lj/cut/coul/cut</I>, and
|
||||
<I>lj/cut/coul/long</I> styles, except that each processor off-loads its
|
||||
<P>The styles with a <I>gpu</I> suffix are identical to the corresponding
|
||||
styles without the suffix, except that each processor off-loads its
|
||||
pairwise calculations to a GPU. Depending on the hardware available
|
||||
on your system this can provide a speed-up. See <A HREF = "doc/Section_accerate.html">this
|
||||
section</A> of the manual for more details.
|
||||
</P>
|
||||
<P>Additional requirements in your input script to run with GPU-enabled
|
||||
styles are as follows:
|
||||
<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
|
||||
|
|
@ -247,17 +246,11 @@ See the <A HREF = "run_style.html">run_style</A> command for details.
|
|||
<P><B>Restrictions:</B>
|
||||
</P>
|
||||
<P>The <I>lj/cut/coul/long</I> and <I>lj/cut/coul/long/tip4p</I> styles are part of
|
||||
the "kspace" package. The <I>lj/cut/gpu</I>, <I>lj/cut/coul/cut/gpu</I>, and
|
||||
<I>lj/cut/coul/long/gpu</I> styles are part of the "gpu"
|
||||
package. The <I>lj/cut/opt</I> style is part of the "opt" package. They
|
||||
are only enabled if LAMMPS was built with those packages. See the
|
||||
<A HREF = "Section_start.html#2_3">Making LAMMPS</A> section for more info. Note
|
||||
that the "kspace" package is installed by default.
|
||||
</P>
|
||||
<P>On some 64-bit machines, compiling with -O3 appears to break the
|
||||
Coulombic tabling option used by the <I>lj/cut/coul/long</I> style. See
|
||||
the "Additional build tips" section of the Making LAMMPS documentation
|
||||
pages for workarounds on this issue.
|
||||
the "kspace" package. The styles with an <I>opt</I> or <I>gpu</I> suffix are
|
||||
part of the "opt" or "gpu" packages. They are only enabled if LAMMPS
|
||||
was built with those packages. See the <A HREF = "Section_start.html#2_3">Making
|
||||
LAMMPS</A> section for more info. Note that the
|
||||
kspace package is installed by default.
|
||||
</P>
|
||||
<P><B>Related commands:</B>
|
||||
</P>
|
||||
|
|
|
|||
|
|
@ -178,20 +178,19 @@ Coulombic cutoff specified in the pair_style command.
|
|||
|
||||
:line
|
||||
|
||||
The {lj/cut/opt} style is identical to the {lj/cut} style, except that
|
||||
it is written in an optimized fashion for faster CPU execution. See
|
||||
"this section"_doc/Section_accerate.html of the manual for more
|
||||
details.
|
||||
The styles with an {opt} suffix are identical to the corresponding
|
||||
styles without the suffix, except that it is written in an optimized
|
||||
fashion for faster CPU execution. See "this
|
||||
section"_doc/Section_accerate.html of the manual for more details.
|
||||
|
||||
The {lj/cut/gpu}, {lj/cut/coul/cut/gpu}, and {lj/cut/coul/long/gpu}
|
||||
styles are identical to the {lj/cut}, {lj/cut/coul/cut}, and
|
||||
{lj/cut/coul/long} styles, except that each processor off-loads its
|
||||
The styles with a {gpu} suffix are identical to the corresponding
|
||||
styles without the suffix, except that each processor off-loads its
|
||||
pairwise calculations to a GPU. Depending on the hardware available
|
||||
on your system this can provide a speed-up. See "this
|
||||
section"_doc/Section_accerate.html of the manual for more details.
|
||||
|
||||
Additional requirements in your input script to run with GPU-enabled
|
||||
styles are as follows:
|
||||
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
|
||||
|
|
@ -236,17 +235,11 @@ See the "run_style"_run_style.html command for details.
|
|||
[Restrictions:]
|
||||
|
||||
The {lj/cut/coul/long} and {lj/cut/coul/long/tip4p} styles are part of
|
||||
the "kspace" package. The {lj/cut/gpu}, {lj/cut/coul/cut/gpu}, and
|
||||
{lj/cut/coul/long/gpu} styles are part of the "gpu"
|
||||
package. The {lj/cut/opt} style is part of the "opt" package. They
|
||||
are only enabled if LAMMPS was built with those packages. See the
|
||||
"Making LAMMPS"_Section_start.html#2_3 section for more info. Note
|
||||
that the "kspace" package is installed by default.
|
||||
|
||||
On some 64-bit machines, compiling with -O3 appears to break the
|
||||
Coulombic tabling option used by the {lj/cut/coul/long} style. See
|
||||
the "Additional build tips" section of the Making LAMMPS documentation
|
||||
pages for workarounds on this issue.
|
||||
the "kspace" package. The styles with an {opt} or {gpu} suffix are
|
||||
part of the "opt" or "gpu" packages. They are only enabled if LAMMPS
|
||||
was built with those packages. See the "Making
|
||||
LAMMPS"_Section_start.html#2_3 section for more info. Note that the
|
||||
kspace package is installed by default.
|
||||
|
||||
[Related commands:]
|
||||
|
||||
|
|
|
|||
|
|
@ -54,18 +54,18 @@ cutoff specified in the pair_style command is used.
|
|||
</P>
|
||||
<HR>
|
||||
|
||||
<P>The <I>lj96/cut/gpu</I> style is identical to the <I>lj96/cut</I> style, except
|
||||
that each processor off-loads its pairwise calculations to a GPU.
|
||||
Depending on the hardware available on your system this can provide a
|
||||
speed-up. See <A HREF = "doc/Section_accerate.html">this section</A> of the manual
|
||||
for more details.
|
||||
<P>The styles with a <I>gpu</I> suffix are identical to the corresponding
|
||||
styles without the suffix, except that each processor off-loads its
|
||||
pairwise calculations to a GPU. Depending on the hardware available
|
||||
on your system this can provide a speed-up. See <A HREF = "doc/Section_accerate.html">this
|
||||
section</A> of the manual for more details.
|
||||
</P>
|
||||
<P>Additional requirements in your input script to run with the
|
||||
<I>lj96/cut/gpu</I> style are as follows:
|
||||
<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
|
||||
selection and initialization steps.
|
||||
</P>
|
||||
<HR>
|
||||
|
||||
|
|
@ -100,8 +100,8 @@ details.
|
|||
|
||||
<P><B>Restrictions:</B>
|
||||
</P>
|
||||
<P>The <I>lj96/cut/gpu</I> style is part of the "gpu" package. It
|
||||
is only enabled if LAMMPS is built with this packages. See the
|
||||
<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><B>Related commands:</B>
|
||||
|
|
|
|||
|
|
@ -50,18 +50,18 @@ cutoff specified in the pair_style command is used.
|
|||
|
||||
:line
|
||||
|
||||
The {lj96/cut/gpu} style is identical to the {lj96/cut} style, except
|
||||
that each processor off-loads its pairwise calculations to a GPU.
|
||||
Depending on the hardware available on your system this can provide a
|
||||
speed-up. See "this section"_doc/Section_accerate.html of the manual
|
||||
for more details.
|
||||
The styles with a {gpu} suffix are identical to the corresponding
|
||||
styles without the suffix, except that each processor off-loads its
|
||||
pairwise calculations to a GPU. Depending on the hardware available
|
||||
on your system this can provide a speed-up. See "this
|
||||
section"_doc/Section_accerate.html of the manual for more details.
|
||||
|
||||
Additional requirements in your input script to run with the
|
||||
{lj96/cut/gpu} style are as follows:
|
||||
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
|
||||
selection and initialization steps.
|
||||
|
||||
:line
|
||||
|
||||
|
|
@ -96,8 +96,8 @@ details.
|
|||
|
||||
[Restrictions:]
|
||||
|
||||
The {lj96/cut/gpu} style is part of the "gpu" package. It
|
||||
is only enabled if LAMMPS is built with this packages. See the
|
||||
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:]
|
||||
|
|
|
|||
|
|
@ -142,11 +142,6 @@ details.
|
|||
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>On some 64-bit machines, compiling with -O3 appears to break the
|
||||
Coulombic tabling option used by the <I>lj/coul</I> style. See the
|
||||
"Additional build tips" section of the Making LAMMPS documentation
|
||||
pages for workarounds on this issue.
|
||||
</P>
|
||||
<P><B>Related commands:</B>
|
||||
</P>
|
||||
<P><A HREF = "pair_coeff.html">pair_coeff</A>
|
||||
|
|
|
|||
|
|
@ -134,11 +134,6 @@ This style is part of the "user-ewaldn" package. It is only enabled
|
|||
if LAMMPS was built with that package. See the "Making
|
||||
LAMMPS"_Section_start.html#2_3 section for more info.
|
||||
|
||||
On some 64-bit machines, compiling with -O3 appears to break the
|
||||
Coulombic tabling option used by the {lj/coul} style. See the
|
||||
"Additional build tips" section of the Making LAMMPS documentation
|
||||
pages for workarounds on this issue.
|
||||
|
||||
[Related commands:]
|
||||
|
||||
"pair_coeff"_pair_coeff.html
|
||||
|
|
|
|||
|
|
@ -58,17 +58,17 @@ See more details below.
|
|||
</P>
|
||||
<HR>
|
||||
|
||||
<P>The <I>lj/expand/gpu</I> style is identical to the <I>lj/expand</I> style,
|
||||
except that each processor off-loads its pairwise calculations to a
|
||||
GPU. Depending on the hardware available on your system this can
|
||||
provide a speed-up. See <A HREF = "doc/Section_accerate.html">this section</A> of
|
||||
the manual for more details.
|
||||
<P>The styles with a <I>gpu</I> suffix are identical to the corresponding
|
||||
styles without the suffix, except that each processor off-loads its
|
||||
pairwise calculations to a GPU. Depending on the hardware available
|
||||
on your system this can provide a speed-up. See <A HREF = "doc/Section_accerate.html">this
|
||||
section</A> of the manual for more details.
|
||||
</P>
|
||||
<P>Additional requirements in your input script to run with GPU-enabled
|
||||
styles are as follows:
|
||||
<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
|
||||
gpu</A> command must be used. The fix controls the GPU
|
||||
selection and initialization steps.
|
||||
</P>
|
||||
<HR>
|
||||
|
|
@ -104,9 +104,9 @@ to be specified in an input script that reads a restart file.
|
|||
|
||||
<P><B>Restrictions:</B>
|
||||
</P>
|
||||
<P>The <I>lj/expand/gpu</I> style is part of the "gpu" package. It is only
|
||||
enabled if LAMMPS was built with that package. See the <A HREF = "Section_start.html#2_3">Making
|
||||
LAMMPS</A> section for more info.
|
||||
<P>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><B>Related commands:</B>
|
||||
</P>
|
||||
|
|
|
|||
|
|
@ -53,17 +53,17 @@ See more details below.
|
|||
|
||||
:line
|
||||
|
||||
The {lj/expand/gpu} style is identical to the {lj/expand} style,
|
||||
except that each processor off-loads its pairwise calculations to a
|
||||
GPU. Depending on the hardware available on your system this can
|
||||
provide a speed-up. See "this section"_doc/Section_accerate.html of
|
||||
the manual for more details.
|
||||
The styles with a {gpu} suffix are identical to the corresponding
|
||||
styles without the suffix, except that each processor off-loads its
|
||||
pairwise calculations to a GPU. Depending on the hardware available
|
||||
on your system this can provide a speed-up. See "this
|
||||
section"_doc/Section_accerate.html of the manual for more details.
|
||||
|
||||
Additional requirements in your input script to run with GPU-enabled
|
||||
styles are as follows:
|
||||
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
|
||||
gpu"_fix_gpu.html command must be used. The fix controls the GPU
|
||||
selection and initialization steps.
|
||||
|
||||
:line
|
||||
|
|
@ -99,9 +99,9 @@ This pair style can only be used via the {pair} keyword of the
|
|||
|
||||
[Restrictions:]
|
||||
|
||||
The {lj/expand/gpu} style is part of the "gpu" package. It is only
|
||||
enabled if LAMMPS was built with that package. See the "Making
|
||||
LAMMPS"_Section_start.html#2_3 section for more info.
|
||||
The 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:]
|
||||
|
||||
|
|
|
|||
|
|
@ -62,19 +62,19 @@ See more details below.
|
|||
</P>
|
||||
<HR>
|
||||
|
||||
<P>The <I>morse/opt</I> style is identical to the <I>morse/cut</I> style, except
|
||||
that it is written in an optimized fashion for faster CPU execution.
|
||||
See <A HREF = "doc/Section_accerate.html">this section</A> of the manual for more
|
||||
details.
|
||||
<P>The styles with an <I>opt</I> suffix are identical to the corresponding
|
||||
styles without the suffix, except that it is written in an optimized
|
||||
fashion for faster CPU execution. See <A HREF = "doc/Section_accerate.html">this
|
||||
section</A> of the manual for more details.
|
||||
</P>
|
||||
<P>The <I>morse/gpu</I> style is identical to the <I>morse</I> style, except that
|
||||
each processor off-loads its pairwise calculations to a GPU.
|
||||
Depending on the hardware available on your system this can provide a
|
||||
speed-up. See <A HREF = "doc/Section_accerate.html">this section</A> of the manual
|
||||
for more details.
|
||||
<P>The styles with a <I>gpu</I> suffix are identical to the corresponding
|
||||
styles without the suffix, except that each processor off-loads its
|
||||
pairwise calculations to a GPU. Depending on the hardware available
|
||||
on your system this can provide a speed-up. See <A HREF = "doc/Section_accerate.html">this
|
||||
section</A> of the manual for more details.
|
||||
</P>
|
||||
<P>Additional requirements in your input script to run with GPU-enabled
|
||||
styles are as follows:
|
||||
<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
|
||||
|
|
@ -109,10 +109,10 @@ to be specified in an input script that reads a restart file.
|
|||
|
||||
<P><B>Restrictions:</B>
|
||||
</P>
|
||||
<P>The <I>morse/opt</I> style is part of the "opt" package. The <I>morse/gpu</I>
|
||||
style is 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>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><B>Related commands:</B>
|
||||
</P>
|
||||
|
|
|
|||
|
|
@ -55,19 +55,19 @@ See more details below.
|
|||
|
||||
:line
|
||||
|
||||
The {morse/opt} style is identical to the {morse/cut} style, except
|
||||
that it is written in an optimized fashion for faster CPU execution.
|
||||
See "this section"_doc/Section_accerate.html of the manual for more
|
||||
details.
|
||||
The styles with an {opt} suffix are identical to the corresponding
|
||||
styles without the suffix, except that it is written in an optimized
|
||||
fashion for faster CPU execution. See "this
|
||||
section"_doc/Section_accerate.html of the manual for more details.
|
||||
|
||||
The {morse/gpu} style is identical to the {morse} style, except that
|
||||
each processor off-loads its pairwise calculations to a GPU.
|
||||
Depending on the hardware available on your system this can provide a
|
||||
speed-up. See "this section"_doc/Section_accerate.html of the manual
|
||||
for more details.
|
||||
The styles with a {gpu} suffix are identical to the corresponding
|
||||
styles without the suffix, except that each processor off-loads its
|
||||
pairwise calculations to a GPU. Depending on the hardware available
|
||||
on your system this can provide a speed-up. See "this
|
||||
section"_doc/Section_accerate.html of the manual for more details.
|
||||
|
||||
Additional requirements in your input script to run with GPU-enabled
|
||||
styles are as follows:
|
||||
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
|
||||
|
|
@ -102,10 +102,10 @@ These pair styles can only be used via the {pair} keyword of the
|
|||
|
||||
[Restrictions:]
|
||||
|
||||
The {morse/opt} style is part of the "opt" package. The {morse/gpu}
|
||||
style is 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.
|
||||
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:]
|
||||
|
||||
|
|
|
|||
|
|
@ -11,15 +11,19 @@
|
|||
|
||||
<H3>pair_style resquared command
|
||||
</H3>
|
||||
<H3>pair_style resquared/gpu command
|
||||
</H3>
|
||||
<P><B>Syntax:</B>
|
||||
</P>
|
||||
<PRE>pair_style resquared cutoff
|
||||
<PRE>pair_style style cutoff
|
||||
</PRE>
|
||||
<UL><LI>cutoff = global cutoff for interactions (distance units)
|
||||
<UL><LI>style = <I>resquared</I> or <I>resquared/gpu</I>
|
||||
<LI>cutoff = global cutoff for interactions (distance units)
|
||||
</UL>
|
||||
<P><B>Examples:</B>
|
||||
</P>
|
||||
<PRE>pair_style resquared 10.0
|
||||
pair_style resquared/gpu 10.0
|
||||
pair_coeff * * 1.0 1.0 1.7 3.4 3.4 1.0 1.0 1.0
|
||||
</PRE>
|
||||
<P><B>Description:</B>
|
||||
|
|
@ -32,6 +36,9 @@ of small spheres of size sigma. LJ particles are a single sphere of
|
|||
size sigma. The distinction is made to allow the pair style to make
|
||||
efficient calculations of ellipsoid/solvent interactions.
|
||||
</P>
|
||||
<P>Style <I>resquared/gpu</I> is a GPU-enabled version of style <I>resquared</I>.
|
||||
See more details below.
|
||||
</P>
|
||||
<P>Details for the equations used are given in the references below and
|
||||
in <A HREF = "PDF/pair_resquared_extra.pdf">this supplementary document</A>.
|
||||
</P>
|
||||
|
|
@ -143,6 +150,21 @@ specified in the pair_style command is used.
|
|||
</P>
|
||||
<HR>
|
||||
|
||||
<P>The styles with a <I>gpu</I> suffix are identical to the corresponding
|
||||
styles without the suffix, except that each processor off-loads its
|
||||
pairwise calculations to a GPU. Depending on the hardware available
|
||||
on your system this can provide a speed-up. See <A HREF = "doc/Section_accerate.html">this
|
||||
section</A> of the manual for more details.
|
||||
</P>
|
||||
<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>
|
||||
<HR>
|
||||
|
||||
<P><B>Mixing, shift, table, tail correction, restart, rRESPA info</B>:
|
||||
</P>
|
||||
<P>For atom type pairs I,J and I != J, the epsilon and sigma coefficients
|
||||
|
|
@ -181,8 +203,9 @@ command</A>.
|
|||
|
||||
<P><B>Restrictions:</B>
|
||||
</P>
|
||||
<P>This style is part of the "asphere" package. It is only enabled if
|
||||
LAMMPS was built with that package. See the <A HREF = "Section_start.html#2_3">Making
|
||||
<P>This style is part of the "asphere" package. The styles with a <I>gpu</I>
|
||||
suffix are part of the "gpu" package. They are only enabled if LAMMPS
|
||||
was built with those packages. See the <A HREF = "Section_start.html#2_3">Making
|
||||
LAMMPS</A> section for more info.
|
||||
</P>
|
||||
<P>This pair style requires that atoms be ellipsoids as defined by the
|
||||
|
|
|
|||
|
|
@ -7,16 +7,19 @@
|
|||
:line
|
||||
|
||||
pair_style resquared command :h3
|
||||
pair_style resquared/gpu command :h3
|
||||
|
||||
[Syntax:]
|
||||
|
||||
pair_style resquared cutoff :pre
|
||||
pair_style style cutoff :pre
|
||||
|
||||
style = {resquared} or {resquared/gpu}
|
||||
cutoff = global cutoff for interactions (distance units) :ul
|
||||
|
||||
[Examples:]
|
||||
|
||||
pair_style resquared 10.0
|
||||
pair_style resquared/gpu 10.0
|
||||
pair_coeff * * 1.0 1.0 1.7 3.4 3.4 1.0 1.0 1.0 :pre
|
||||
|
||||
[Description:]
|
||||
|
|
@ -29,6 +32,9 @@ of small spheres of size sigma. LJ particles are a single sphere of
|
|||
size sigma. The distinction is made to allow the pair style to make
|
||||
efficient calculations of ellipsoid/solvent interactions.
|
||||
|
||||
Style {resquared/gpu} is a GPU-enabled version of style {resquared}.
|
||||
See more details below.
|
||||
|
||||
Details for the equations used are given in the references below and
|
||||
in "this supplementary document"_PDF/pair_resquared_extra.pdf.
|
||||
|
||||
|
|
@ -140,6 +146,21 @@ specified in the pair_style command is used.
|
|||
|
||||
:line
|
||||
|
||||
The styles with a {gpu} suffix are identical to the corresponding
|
||||
styles without the suffix, except that each processor off-loads its
|
||||
pairwise calculations to a GPU. Depending on the hardware available
|
||||
on your system this can provide a speed-up. See "this
|
||||
section"_doc/Section_accerate.html of the manual for more details.
|
||||
|
||||
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.
|
||||
|
||||
:line
|
||||
|
||||
[Mixing, shift, table, tail correction, restart, rRESPA info]:
|
||||
|
||||
For atom type pairs I,J and I != J, the epsilon and sigma coefficients
|
||||
|
|
@ -178,8 +199,9 @@ command"_run_style.html.
|
|||
|
||||
[Restrictions:]
|
||||
|
||||
This style is part of the "asphere" package. It is only enabled if
|
||||
LAMMPS was built with that package. See the "Making
|
||||
This style is part of the "asphere" package. The styles with a {gpu}
|
||||
suffix are part of the "gpu" package. They are only enabled if LAMMPS
|
||||
was built with those packages. See the "Making
|
||||
LAMMPS"_Section_start.html#2_3 section for more info.
|
||||
|
||||
This pair style requires that atoms be ellipsoids as defined by the
|
||||
|
|
|
|||
|
|
@ -89,7 +89,8 @@ the pair_style command, and coefficients specified by the associated
|
|||
<LI><A HREF = "pair_hybrid.html">pair_style hybrid</A> - multiple styles of pairwise interactions
|
||||
<LI><A HREF = "pair_hybrid.html">pair_style hybrid/overlay</A> - multiple styles of superposed pairwise interactions
|
||||
</UL>
|
||||
<UL><LI><A HREF = "pair_airebo.html">pair_style airebo</A> - AIREBO potential of Stuart
|
||||
<UL><LI><A HREF = "pair_adp.html">pair_style adp</A> - angular dependent potential (ADP) of Mishin
|
||||
<LI><A HREF = "pair_airebo.html">pair_style airebo</A> - AIREBO potential of Stuart
|
||||
<LI><A HREF = "pair_born.html">pair_style born</A> - Born-Mayer-Huggins potential
|
||||
<LI><A HREF = "pair_born.html">pair_style born/coul/long</A> - Born-Mayer-Huggins with long-range Coulomb
|
||||
<LI><A HREF = "pair_buck.html">pair_style buck</A> - Buckingham potential
|
||||
|
|
|
|||
|
|
@ -86,6 +86,7 @@ the pair_style command, and coefficients specified by the associated
|
|||
"pair_style hybrid"_pair_hybrid.html - multiple styles of pairwise interactions
|
||||
"pair_style hybrid/overlay"_pair_hybrid.html - multiple styles of superposed pairwise interactions :ul
|
||||
|
||||
"pair_style adp"_pair_adp.html - angular dependent potential (ADP) of Mishin
|
||||
"pair_style airebo"_pair_airebo.html - AIREBO potential of Stuart
|
||||
"pair_style born"_pair_born.html - Born-Mayer-Huggins potential
|
||||
"pair_style born/coul/long"_pair_born.html - Born-Mayer-Huggins with long-range Coulomb
|
||||
|
|
|
|||
Loading…
Reference in New Issue