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more adjustments to style pages

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This commit is contained in:
Steve Plimpton
2018-11-26 11:24:48 -07:00
parent a010780808
commit bfaa2e9ee1
6 changed files with 37 additions and 92 deletions
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18
doc/src/Run_options.txt
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@ -363,20 +363,20 @@ run:
read_restart restartfile (remap)
write_data datafile keyword value ... :pre
Note that the specified restartfile and/or datafile can have the
wild-card character "*". The restartfile can also have the wild-card
character "%". The meaning of these characters is explained on the
The specified restartfile and/or datafile can have the wild-card
character "*". The restartfile can also have the wild-card character
"%". The meaning of these characters is explained on the
"read_restart"_read_restart.html and "write_data"_write_data.html doc
pages. The use of "%" means that a parallel restart file can be read.
Note that a filename such as file.* will need to be enclosed in quotes
to avoid shell expansion of the "*" character.
Note that following restartfile, the optional word "remap" can be
used. This has the effect of adding it to the
"read_restart"_read_restart.html command, as explained on its doc
page. This is useful if reading the restart file triggers an error
that atoms have been lost. In that case, use of the remap flag should
allow the data file to still be produced.
Following restartfile, the optional word "remap" can be used. This
has the effect of adding it to the "read_restart"_read_restart.html
command, as explained on its doc page. This is useful if reading the
restart file triggers an error that atoms have been lost. In that
case, use of the remap flag should allow the data file to still be
produced.
The syntax following restartfile (or remap), namely

24
doc/src/angle_coeff.txt
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@ -60,26 +60,14 @@ doc page for details.
:line
Here is an alphabetic list of angle styles defined in LAMMPS. Click on
the style to display the formula it computes and coefficients
specified by the associated "angle_coeff"_angle_coeff.html command.
Note that there are also additional angle styles submitted by users
which are included in the LAMMPS distribution. The full list of all
angle styles is on the "Commands bond"_Commands_bond.html#angle doc
The list of all angle styles defined in LAMMPS is given on the
"angle_style"_angle_style.html doc page. They are also listed in more
compact form on the "Commands angle"_Commands_bond.html#angle doc
page.
"angle_style none"_angle_none.html - turn off angle interactions
"angle_style hybrid"_angle_hybrid.html - define multiple styles of angle interactions :ul
"angle_style charmm"_angle_charmm.html - CHARMM angle
"angle_style class2"_angle_class2.html - COMPASS (class 2) angle
"angle_style cosine"_angle_cosine.html - cosine angle potential
"angle_style cosine/delta"_angle_cosine_delta.html - difference of cosines angle potential
"angle_style cosine/periodic"_angle_cosine_periodic.html - DREIDING angle
"angle_style cosine/squared"_angle_cosine_squared.html - cosine squared angle potential
"angle_style harmonic"_angle_harmonic.html - harmonic angle
"angle_style table"_angle_table.html - tabulated by angle :ul
On either of those pages, click on the style to display the formula it
computes and its coefficients as specified by the associated
angle_coeff command.
:line

24
doc/src/bond_coeff.txt
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@ -56,25 +56,13 @@ corresponds to the 1st example above would be listed as
:line
Here is an alphabetic list of bond styles defined in LAMMPS. Click on
the style to display the formula it computes and coefficients
specified by the associated "bond_coeff"_bond_coeff.html command.
The list of all bond styles defined in LAMMPS is given on the
"bond_style"_bond_style.html doc page. They are also listed in more
compact form on the "Commands bond"_Commands_bond.html doc page.
Note that here are also additional bond styles submitted by users
which are included in the LAMMPS distribution. The full list of all
bond styles is on the "Commands bond"_Commands_bond.html doc page.
"bond_style none"_bond_none.html - turn off bonded interactions
"bond_style hybrid"_bond_hybrid.html - define multiple styles of bond interactions :ul
"bond_style class2"_bond_class2.html - COMPASS (class 2) bond
"bond_style fene"_bond_fene.html - FENE (finite-extensible non-linear elastic) bond
"bond_style fene/expand"_bond_fene_expand.html - FENE bonds with variable size particles
"bond_style harmonic"_bond_harmonic.html - harmonic bond
"bond_style morse"_bond_morse.html - Morse bond
"bond_style nonlinear"_bond_nonlinear.html - nonlinear bond
"bond_style quartic"_bond_quartic.html - breakable quartic bond
"bond_style table"_bond_table.html - tabulated by bond length :ul
On either of those pages, click on the style to display the formula it
computes and its coefficients as specified by the associated
bond_coeff command.
:line

24
doc/src/dihedral_coeff.txt
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@ -69,24 +69,14 @@ necessary.
:line
Here is an alphabetic list of dihedral styles defined in LAMMPS. Click on
the style to display the formula it computes and coefficients
specified by the associated "dihedral_coeff"_dihedral_coeff.html command.
The list of all dihedral styles defined in LAMMPS is given on the
"dihedral_style"_dihedral_style.html doc page. They are also listed
in more compact form on the "Commands
dihedral"_Commands_bond.html#dihedral doc page.
Note that there are also additional dihedral styles submitted by users
which are included in the LAMMPS distribution. The full list of all
dihedral styles is on the "Commands bond"_Commands_bond.html#dihedral
doc page.
"dihedral_style none"_dihedral_none.html - turn off dihedral interactions
"dihedral_style hybrid"_dihedral_hybrid.html - define multiple styles of dihedral interactions :ul
"dihedral_style charmm"_dihedral_charmm.html - CHARMM dihedral
"dihedral_style class2"_dihedral_class2.html - COMPASS (class 2) dihedral
"dihedral_style harmonic"_dihedral_harmonic.html - harmonic dihedral
"dihedral_style helix"_dihedral_helix.html - helix dihedral
"dihedral_style multi/harmonic"_dihedral_multi_harmonic.html - multi-harmonic dihedral
"dihedral_style opls"_dihedral_opls.html - OPLS dihedral :ul
On either of those pages, click on the style to display the formula it
computes and its coefficients as specified by the associated
dihedral_coeff command.
:line

22
doc/src/improper_coeff.txt
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@ -62,22 +62,14 @@ page for details.
:line
Here is an alphabetic list of improper styles defined in LAMMPS. Click on
the style to display the formula it computes and coefficients
specified by the associated "improper_coeff"_improper_coeff.html command.
The list of all improper styles defined in LAMMPS is given on the
"improper_style"_improper_style.html doc page. They are also listed
in more compact form on the "Commands
improper"_Commands_bond.html#improper doc page.
Note that there are also additional improper styles submitted by users
which are included in the LAMMPS distribution. The full list of all
improper styles is on the "Commands bond"_Commands_bond.html#improper
doc page.
"improper_style none"_improper_none.html - turn off improper interactions
"improper_style hybrid"_improper_hybrid.html - define multiple styles of improper interactions :ul
"improper_style class2"_improper_class2.html - COMPASS (class 2) improper
"improper_style cvff"_improper_cvff.html - CVFF improper
"improper_style harmonic"_improper_harmonic.html - harmonic improper
"improper_style umbrella"_improper_umbrella.html - DREIDING improper :ul
On either of those pages, click on the style to display the formula it
computes and its coefficients as specified by the associated
improper_coeff command.
:line

17
doc/src/pair_coeff.txt
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@ -114,21 +114,8 @@ The alphabetic list of pair styles defined in LAMMPS is given on the
"pair_style"_pair_style.html doc page. They are also listed in more
compact form on the "Commands pair"_Commands_pair.html doc page.
Click on the style to display the formula it computes, arguments
specified in the pair_style command, and coefficients specified by the
associated "pair_coeff"_pair_coeff.html command.
Note that there are also additional pair styles (not listed on the
"pair_style"_pair_style.html doc page) submitted by users which are
included in the LAMMPS distribution. The full list of all pair styles
is on the "Commands pair"_Commands_pair.html doc page.
There are also additional accelerated pair styles (not listed on the
"pair_style"_pair_style.html doc page) included in the LAMMPS
distribution for faster performance on CPUs, GPUs, and KNLs. The
individual style names on the "Commands pair"_Commands_pair.html doc
page are followed by one or more of (g,i,k,o,t) to indicate which
accelerated styles exist.
Click on the style to display the formula it computes and its
coefficients as specified by the associated pair_coeff command.
:line