replace :ule,l and :ole,l with :l<br>:ule and :l<br>:ole
This commit is contained in:
@ -47,7 +47,8 @@ it to be part of every patch. :l
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There is also a "Developer.pdf"_Developer.pdf file in the doc
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directory, which describes the internal structure and algorithms of
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LAMMPS. :ule,l
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LAMMPS. :l
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:ule
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LAMMPS stands for Large-scale Atomic/Molecular Massively Parallel
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Simulator.
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@ -28,8 +28,9 @@ multi-core CPUs, GPUs, and Intel Xeon Phi coprocessors.
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5.3.2 "USER-INTEL package"_accelerate_intel.html :l
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5.3.3 "KOKKOS package"_accelerate_kokkos.html :l
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5.3.4 "USER-OMP package"_accelerate_omp.html :l
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5.3.5 "OPT package"_accelerate_opt.html :l,ule
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5.4 "Comparison of various accelerator packages"_#acc_4 :l,ule
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5.3.5 "OPT package"_accelerate_opt.html :l
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5.4 "Comparison of various accelerator packages"_#acc_4 :l
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:ule
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The "Benchmark page"_http://lammps.sandia.gov/bench.html of the LAMMPS
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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
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Cash. Small denominations, unmarked bills preferred. Paper sack OK.
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Leave on desk. VISA also accepted. Chocolate chip cookies
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encouraged. :ule,l
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encouraged. :l
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:ule
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:line
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@ -36,7 +36,8 @@ sigma cutoff (7 neighbors per atom), NVE integration :l
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Rhodo = rhodopsin protein in solvated lipid bilayer, CHARMM force
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field with a 10 Angstrom LJ cutoff (440 neighbors per atom),
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particle-particle particle-mesh (PPPM) for long-range Coulombics, NPT
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integration :ole,l
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integration :l
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:ole
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Input files for these 5 problems are provided in the bench directory
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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
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Some force fields reverse the sign convention on {d}. :l
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Some force fields let {n} be positive or negative which corresponds to
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{d} = 1 or -1 for the harmonic style. :ule,l
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{d} = 1 or -1 for the harmonic style. :l
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:ule
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:line
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@ -598,7 +598,8 @@ obviously play movie files directly. Similarly for corresponding tools
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bundled with Linux desktop environments. However, due to licensing
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issues with some file formats, the formats may require installing
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additional libraries, purchasing a license, or may not be
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supported. :ule,l
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supported. :l
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:ule
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:line
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@ -59,7 +59,8 @@ multi-threading :l
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OPT = a handful of pair styles, cache-optimized for faster CPU
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performance :l
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HYBRID = a combination of two packages can be specified (see below) :ule,l
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HYBRID = a combination of two packages can be specified (see below) :l
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:ule
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As an example, all of the packages provide a "pair_style
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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 \
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type of core-Drude bond from equation (1). The timesteps used by these \
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authors are between 0.5 and 2 fs, with the degrees of freedom of the \
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Drude oscillators kept cold at 1 K. :l
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In both these force fields hydrogen atoms are treated as non-polarizable. :ule,l
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In both these force fields hydrogen atoms are treated as non-polarizable. :l
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:ule
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The motion of of the Drude particles can be calculated by minimizing
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@ -104,7 +105,8 @@ due to the short distances, so an atom may capture the Drude particle \
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(shell) of a neighbor, or the induced dipoles within the same molecule \
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may align too much. To avoid this, damping at short of the \
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interactions between the point charges composing the induced dipole \
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can be done by "Thole"_#Thole functions. :ole,l
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can be done by "Thole"_#Thole functions. :l
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:ole
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:line
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