update documentation for dihedral style table/cut

This commit is contained in:
Axel Kohlmeyer
2018-05-11 16:08:23 -04:00
parent 308dac6821
commit 821ef0cf77
4 changed files with 7 additions and 30 deletions

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@ -1212,7 +1212,8 @@ package"_Section_start.html#start_3.
"nharmonic (o)"_dihedral_nharmonic.html, "nharmonic (o)"_dihedral_nharmonic.html,
"quadratic (o)"_dihedral_quadratic.html, "quadratic (o)"_dihedral_quadratic.html,
"spherical (o)"_dihedral_spherical.html, "spherical (o)"_dihedral_spherical.html,
"table (o)"_dihedral_table.html :tb(c=4,ea=c) "table (o)"_dihedral_table.html
"table/cut"_dihedral_table_cut.html :tb(c=4,ea=c)
:line :line

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@ -7,7 +7,6 @@
:line :line
dihedral_style table/cut command :h3 dihedral_style table/cut command :h3
dihedral_style table/cut/omp command :h3
[Syntax:] [Syntax:]
@ -61,9 +60,8 @@ filename
keyword :ul keyword :ul
The cutoff dihedral style uses a tabulated dihedral interaction with a The cutoff dihedral style uses a tabulated dihedral interaction with a
cutoff function cutoff function (TODO: add image of formula here)
:c,image(Eqs/dihedral_table_cut.jpg)
The cutoff specifies an prefactor to the cutoff function. While this value The cutoff specifies an prefactor to the cutoff function. While this value
would ordinarily equal 1 there may be situations where the value should change. would ordinarily equal 1 there may be situations where the value should change.
@ -190,41 +188,17 @@ Note that one file can contain many sections, each with a tabulated
potential. LAMMPS reads the file section by section until it finds one potential. LAMMPS reads the file section by section until it finds one
that matches the specified keyword. that matches the specified keyword.
:line
Styles with a {gpu}, {intel}, {kk}, {omp}, or {opt} suffix are
functionally the same as the corresponding style without the suffix.
They have been optimized to run faster, depending on your available
hardware, as discussed in "Section_accelerate"_Section_accelerate.html
of the manual. The accelerated styles take the same arguments and
should produce the same results, except for round-off and precision
issues.
These accelerated styles are part of the GPU, USER-INTEL, KOKKOS,
USER-OMP and OPT packages, respectively. They are only enabled if
LAMMPS was built with those packages. See the "Making
LAMMPS"_Section_start.html#start_3 section for more info.
You can specify the accelerated styles explicitly in your input script
by including their suffix, or you can use the "-suffix command-line
switch"_Section_start.html#start_6 when you invoke LAMMPS, or you can
use the "suffix"_suffix.html command in your input script.
See "Section_accelerate"_Section_accelerate.html of the manual for
more instructions on how to use the accelerated styles effectively.
[Restrictions:] [Restrictions:]
This dihedral style can only be used if LAMMPS was built with the This dihedral style can only be used if LAMMPS was built with the
USER-MISC package. See the "Making LAMMPS"_Section_start.html#2_3 USER-MISC package. See the "Making LAMMPS"_Section_start.html#start_3
section for more info on packages. section for more info on packages.
[Related commands:] [Related commands:]
"dihedral_coeff"_dihedral_coeff.html "dihedral_coeff"_dihedral_coeff.html, "dihedral_style table"_dihedral_table.html
[Default:] none [Default:] none
:line
:link(dihedralcut-Salerno) :link(dihedralcut-Salerno)
[(Salerno)] Salerno, Bernstein, J Chem Theory Comput, --, ---- (2018). [(Salerno)] Salerno, Bernstein, J Chem Theory Comput, --, ---- (2018).

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@ -19,6 +19,7 @@ Dihedral Styles :h1
dihedral_quadratic dihedral_quadratic
dihedral_spherical dihedral_spherical
dihedral_table dihedral_table
dihedral_table_cut
dihedral_zero dihedral_zero
dihedral_charmm dihedral_charmm
dihedral_class2 dihedral_class2

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@ -582,6 +582,7 @@ dihedral_opls.html
dihedral_quadratic.html dihedral_quadratic.html
dihedral_spherical.html dihedral_spherical.html
dihedral_table.html dihedral_table.html
dihedral_table_cut.html
dihedral_zero.html dihedral_zero.html
lammps_commands_improper.html lammps_commands_improper.html