From 38ce56f2526ec016b59c7add85cb5e0abb2c1937 Mon Sep 17 00:00:00 2001 From: Axel Kohlmeyer Date: Wed, 21 Feb 2018 11:51:25 +0100 Subject: [PATCH] fix documentation issues: non-ASCII characters, broken/missing links, formatting --- doc/src/Section_commands.txt | 1 + doc/src/fix_bond_react.txt | 31 ++++++++++++++++--------------- doc/src/fixes.txt | 1 + doc/src/lammps.book | 1 + 4 files changed, 19 insertions(+), 15 deletions(-) diff --git a/doc/src/Section_commands.txt b/doc/src/Section_commands.txt index 02ce6f2882..7eddcf9fe1 100644 --- a/doc/src/Section_commands.txt +++ b/doc/src/Section_commands.txt @@ -683,6 +683,7 @@ package"_Section_start.html#start_3. "addtorque"_fix_addtorque.html, "atc"_fix_atc.html, "ave/correlate/long"_fix_ave_correlate_long.html, +"bond/react"_fix_bond_react.html, "colvars"_fix_colvars.html, "dpd/energy (k)"_fix_dpd_energy.html, "drude"_fix_drude.html, diff --git a/doc/src/fix_bond_react.txt b/doc/src/fix_bond_react.txt index 8d3cc2e949..3483b79930 100644 --- a/doc/src/fix_bond_react.txt +++ b/doc/src/fix_bond_react.txt @@ -39,7 +39,7 @@ react = mandatory argument indicating new reaction specification fraction = initiate reaction with this probability if otherwise eligible seed = random number seed (positive integer) {stabilize_steps} value = timesteps - timesteps = number of timesteps to apply internally created nve/limit :pre + timesteps = number of timesteps to apply internally created nve/limit.html :pre :ule [Examples:] @@ -85,7 +85,7 @@ with fix/bond react. Only one 'fix bond/react' command can be used at a time. Multiple reactions can be simultaneously applied by specifying multiple 'react' arguments to a single 'fix bond/react' command. This syntax is -necessary because the ‘common keywords’ are applied to all reactions. +necessary because the 'common keywords' are applied to all reactions. The {stabilization} keyword enables reaction site stabilization. Reaction site stabilization is performed by including reacting atoms @@ -178,7 +178,7 @@ description of the file. Lines can have a trailing comment starting with '#' that is ignored. If the line is blank (only whitespace after comment is deleted), it is skipped. If the line contains a header keyword, the corresponding value(s) is read from the line. If it -doesn’t contain a header keyword, the line begins the body of the +doesn't contain a header keyword, the line begins the body of the file. The header contains one mandatory keyword and one optional keyword. @@ -203,8 +203,7 @@ order. The value(s) are read from the beginning of the line. Thus the keyword 'equivalences' should be in a line like "25 equivalences." equivalences = # of atoms in the pre- and post-reacted molecule -templates edgeIDs = # of edge atoms in the pre-reacted molecule -template +templates edgeIDs = # of edge atoms in the pre-reacted molecule template :pre The edgeIDs keyword is optional. @@ -228,21 +227,22 @@ pre-reacted molecule template. A sample map file is given below: ---------------- -this is a map file +:line + +# This is a map file :pre 2 edgeIDs -7 equivalences +7 equivalences :pre -BondingIDs +BondingIDs :pre -3 5 +3 5 :pre -EdgeIDs +EdgeIDs :pre -1 7 +1 7 :pre -Equivalences +Equivalences :pre 1 1 2 2 @@ -250,8 +250,9 @@ Equivalences 4 4 5 5 6 6 -7 7 ---------------- +7 7 :pre + +:line Once a reaction site has been successfully identified, data structures within LAMMPS that store bond topology are updated to reflect the diff --git a/doc/src/fixes.txt b/doc/src/fixes.txt index c3fcc06bf1..fca442cc13 100644 --- a/doc/src/fixes.txt +++ b/doc/src/fixes.txt @@ -23,6 +23,7 @@ Fixes :h1 fix_bond_break fix_bond_create fix_bond_swap + fix_bond_react fix_box_relax fix_cmap fix_colvars diff --git a/doc/src/lammps.book b/doc/src/lammps.book index d4e73453b0..492f42e4d9 100644 --- a/doc/src/lammps.book +++ b/doc/src/lammps.book @@ -150,6 +150,7 @@ fix_aveforce.html fix_balance.html fix_bond_break.html fix_bond_create.html +fix_bond_react.html fix_bond_swap.html fix_box_relax.html fix_cmap.html