replace :ule,l and :ole,l with :l<br>:ule and :l<br>:ole

This commit is contained in:
Axel Kohlmeyer
2016-09-01 02:07:16 -04:00
parent 5e6dff36e4
commit fc093a0aab
8 changed files with 19 additions and 10 deletions

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@ -47,7 +47,8 @@ it to be part of every patch. :l
There is also a "Developer.pdf"_Developer.pdf file in the doc
directory, which describes the internal structure and algorithms of
LAMMPS. :ule,l
LAMMPS. :l
:ule
LAMMPS stands for Large-scale Atomic/Molecular Massively Parallel
Simulator.

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@ -28,8 +28,9 @@ multi-core CPUs, GPUs, and Intel Xeon Phi coprocessors.
5.3.2 "USER-INTEL package"_accelerate_intel.html :l
5.3.3 "KOKKOS package"_accelerate_kokkos.html :l
5.3.4 "USER-OMP package"_accelerate_omp.html :l
5.3.5 "OPT package"_accelerate_opt.html :l,ule
5.4 "Comparison of various accelerator packages"_#acc_4 :l,ule
5.3.5 "OPT package"_accelerate_opt.html :l
5.4 "Comparison of various accelerator packages"_#acc_4 :l
:ule
The "Benchmark page"_http://lammps.sandia.gov/bench.html of the LAMMPS
web site gives performance results for the various accelerator

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@ -460,7 +460,8 @@ Site"_lws. It might be added to the page. No promises. :l
Cash. Small denominations, unmarked bills preferred. Paper sack OK.
Leave on desk. VISA also accepted. Chocolate chip cookies
encouraged. :ule,l
encouraged. :l
:ule
:line

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@ -36,7 +36,8 @@ sigma cutoff (7 neighbors per atom), NVE integration :l
Rhodo = rhodopsin protein in solvated lipid bilayer, CHARMM force
field with a 10 Angstrom LJ cutoff (440 neighbors per atom),
particle-particle particle-mesh (PPPM) for long-range Coulombics, NPT
integration :ole,l
integration :l
:ole
Input files for these 5 problems are provided in the bench directory
of the LAMMPS distribution. Each has 32,000 atoms and runs for 100

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@ -45,7 +45,8 @@ in some force fields trans = 0 degrees. :ulb,l
Some force fields reverse the sign convention on {d}. :l
Some force fields let {n} be positive or negative which corresponds to
{d} = 1 or -1 for the harmonic style. :ule,l
{d} = 1 or -1 for the harmonic style. :l
:ule
:line

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@ -598,7 +598,8 @@ obviously play movie files directly. Similarly for corresponding tools
bundled with Linux desktop environments. However, due to licensing
issues with some file formats, the formats may require installing
additional libraries, purchasing a license, or may not be
supported. :ule,l
supported. :l
:ule
:line

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@ -59,7 +59,8 @@ multi-threading :l
OPT = a handful of pair styles, cache-optimized for faster CPU
performance :l
HYBRID = a combination of two packages can be specified (see below) :ule,l
HYBRID = a combination of two packages can be specified (see below) :l
:ule
As an example, all of the packages provide a "pair_style
lj/cut"_pair_lj.html variant, with style names lj/cut/opt, lj/cut/omp,

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@ -67,7 +67,8 @@ for all Drude particles, and to calculate the force constant for each \
type of core-Drude bond from equation (1). The timesteps used by these \
authors are between 0.5 and 2 fs, with the degrees of freedom of the \
Drude oscillators kept cold at 1 K. :l
In both these force fields hydrogen atoms are treated as non-polarizable. :ule,l
In both these force fields hydrogen atoms are treated as non-polarizable. :l
:ule
The motion of of the Drude particles can be calculated by minimizing
@ -104,7 +105,8 @@ due to the short distances, so an atom may capture the Drude particle \
(shell) of a neighbor, or the induced dipoles within the same molecule \
may align too much. To avoid this, damping at short of the \
interactions between the point charges composing the induced dipole \
can be done by "Thole"_#Thole functions. :ole,l
can be done by "Thole"_#Thole functions. :l
:ole
:line