Merge pull request #386 from akohlmey/doc-consistentcy (020e75e7) · Commits · 郑智淋 / lammps

doc/src/Section_commands.txt

+4 −4

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		@@ -281,12 +281,12 @@ the "minimize"_minimize.html command. A parallel tempering

		3.4 Commands listed by category :link(cmd_4),h4

		This section lists all LAMMPS commands, grouped by category. The
		"next section"_#cmd_5 lists the same commands alphabetically. The
		This section lists core LAMMPS commands, grouped by category.
		The "next section"_#cmd_5 lists all commands alphabetically. The
		next section also includes (long) lists of style options for entries
		that appear in the following categories as a single command (fix,
		compute, pair, etc). Commands that are added by user packages are not
		included in these categories, but they are in the next section.
		included in the categories here, but they are in the next section.

		Initialization:

		@@ -1091,7 +1091,7 @@ package"_Section_start.html#start_3.

		"harmonic/shift (o)"_bond_harmonic_shift.html,
		"harmonic/shift/cut (o)"_bond_harmonic_shift_cut.html,
		"oxdna/fene"_bond_oxdna_fene.html :tb(c=4,ea=c)
		"oxdna/fene"_bond_oxdna.html :tb(c=4,ea=c)

		:line

doc/src/Section_packages.txt

+4 −4

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		@@ -1295,13 +1295,13 @@ integrators with improved stability.

		See these doc pages to get started:

		"bond_style oxdna_fene"_bond_oxdna_fene.html
		"pair_style oxdna_excv"_pair_oxdna_excv.html
		"bond_style oxdna/fene"_bond_oxdna.html
		"pair_style oxdna/..."_pair_oxdna.html
		"fix nve/dotc/langevin"_fix_nve_dotc_langevin.html :ul

		Supporting info: /src/USER-CGDNA/README, "bond_style
		oxdna_fene"_bond_oxdna_fene.html, "pair_style
		oxdna_excv"_pair_oxdna_excv.html, "fix
		oxdna/fene"_bond_oxdna.html, "pair_style
		oxdna/..."_pair_oxdna.html, "fix
		nve/dotc/langevin"_fix_nve_dotc_langevin.html

		Author: Oliver Henrich at the University of Edinburgh, UK (o.henrich

doc/src/bond_oxdna_fene.txt→doc/src/bond_oxdna.txt

+10 −10

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		@@ -6,20 +6,20 @@

		:line

		bond_style oxdna_fene command :h3
		bond_style oxdna/fene command :h3

		[Syntax:]

		bond_style oxdna_fene :pre
		bond_style oxdna/fene :pre

		[Examples:]

		bond_style oxdna_fene
		bond_style oxdna/fene
		bond_coeff * 2.0 0.25 0.7525 :pre

		[Description:]

		The {oxdna_fene} bond style uses the potential
		The {oxdna/fene} bond style uses the potential

		:c,image(Eqs/bond_oxdna_fene.jpg)

		@@ -37,14 +37,14 @@ Delta (distance)
		r0 (distance) :ul

		NOTE: This bond style has to be used together with the corresponding oxDNA pair styles
		for excluded volume interaction {oxdna_excv}, stacking {oxdna_stk}, cross-stacking {oxdna_xstk}
		and coaxial stacking interaction {oxdna_coaxstk} as well as hydrogen-bonding interaction {oxdna_hbond} (see also documentation of
		"pair_style oxdna_excv"_pair_oxdna_excv.html). The coefficients
		for excluded volume interaction {oxdna/excv}, stacking {oxdna/stk}, cross-stacking {oxdna/xstk}
		and coaxial stacking interaction {oxdna/coaxstk} as well as hydrogen-bonding interaction {oxdna/hbond} (see also documentation of
		"pair_style oxdna/excv"_pair_oxdna.html). The coefficients
		in the above example have to be kept fixed and cannot be changed without reparametrizing the entire model.

		Example input and data files can be found in /examples/USER/cgdna/examples/duplex1/ and /duplex2/.
		Example input and data files can be found in examples/USER/cgdna/examples/duplex1/ and /duplex2/.
		A simple python setup tool which creates single straight or helical DNA strands,
		DNA duplexes or arrays of DNA duplexes can be found in /examples/USER/cgdna/util/.
		DNA duplexes or arrays of DNA duplexes can be found in examples/USER/cgdna/util/.
		A technical report with more information on the model, the structure of the input file,
		the setup tool and the performance of the LAMMPS-implementation of oxDNA
		can be found "here"_PDF/USER-CGDNA-overview.pdf.
		@@ -60,7 +60,7 @@ LAMMPS"_Section_start.html#start_3 section for more info on packages.

		[Related commands:]

		"pair_style oxdna_excv"_pair_oxdna_excv.html, "fix nve/dotc/langevin"_fix_nve_dotc_langevin.html, "bond_coeff"_bond_coeff.html
		"pair_style oxdna/excv"_pair_oxdna.html, "fix nve/dotc/langevin"_fix_nve_dotc_langevin.html, "bond_coeff"_bond_coeff.html

		[Default:] none

doc/src/bonds.txt

+1 −1

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		@@ -15,7 +15,7 @@ Bond Styles :h1
		bond_morse
		bond_none
		bond_nonlinear
		bond_oxdna_fene
		bond_oxdna
		bond_quartic
		bond_table
		bond_zero

doc/src/fix_bond_break.txt

+2 −2

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		@@ -79,8 +79,8 @@ part of bonds, angles, etc.

		NOTE: One data structure that is not updated when a bond breaks are
		the molecule IDs stored by each atom. Even though one molecule
		becomes two moleclues due to the broken bond, all atoms in both new
		moleclues retain their original molecule IDs.
		becomes two molecules due to the broken bond, all atoms in both new
		molecules retain their original molecule IDs.

		Computationally, each timestep this fix operates, it loops over all
		the bonds in the system and computes distances between pairs of bonded

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