From 20a9ffe69dfd16943e13f41280a3ccb31af0f747 Mon Sep 17 00:00:00 2001
From: Axel Kohlmeyer <akohlmey@gmail.com>
Date: Tue, 21 Feb 2017 21:27:34 -0500
Subject: [PATCH] improve consistency and resolve dead links for USER-CGDNA
related doc files
---
doc/src/Section_commands.txt | 2 +-
doc/src/Section_packages.txt | 8 ++--
.../{bond_oxdna_fene.txt => bond_oxdna.txt} | 20 ++++-----
doc/src/bonds.txt | 2 +-
.../{pair_oxdna_excv.txt => pair_oxdna.txt} | 44 +++++++++----------
doc/src/pairs.txt | 2 +-
6 files changed, 39 insertions(+), 39 deletions(-)
rename doc/src/{bond_oxdna_fene.txt => bond_oxdna.txt} (69%)
rename doc/src/{pair_oxdna_excv.txt => pair_oxdna.txt} (64%)
diff --git a/doc/src/Section_commands.txt b/doc/src/Section_commands.txt
index c36c961de3..6812c5d1d2 100644
--- a/doc/src/Section_commands.txt
+++ b/doc/src/Section_commands.txt
@@ -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
diff --git a/doc/src/Section_packages.txt b/doc/src/Section_packages.txt
index b9b96d66ad..fcde05a75b 100644
--- a/doc/src/Section_packages.txt
+++ b/doc/src/Section_packages.txt
@@ -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
diff --git a/doc/src/bond_oxdna_fene.txt b/doc/src/bond_oxdna.txt
similarity index 69%
rename from doc/src/bond_oxdna_fene.txt
rename to doc/src/bond_oxdna.txt
index 23018c2ab7..3a10058812 100644
--- a/doc/src/bond_oxdna_fene.txt
+++ b/doc/src/bond_oxdna.txt
@@ -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
diff --git a/doc/src/bonds.txt b/doc/src/bonds.txt
index ee35672aa1..169d56ecbe 100644
--- a/doc/src/bonds.txt
+++ b/doc/src/bonds.txt
@@ -15,7 +15,7 @@ Bond Styles :h1
bond_morse
bond_none
bond_nonlinear
- bond_oxdna_fene
+ bond_oxdna
bond_quartic
bond_table
bond_zero
diff --git a/doc/src/pair_oxdna_excv.txt b/doc/src/pair_oxdna.txt
similarity index 64%
rename from doc/src/pair_oxdna_excv.txt
rename to doc/src/pair_oxdna.txt
index 23a727b3b9..ba2a3e4b01 100644
--- a/doc/src/pair_oxdna_excv.txt
+++ b/doc/src/pair_oxdna.txt
@@ -6,36 +6,36 @@
:line
-pair_style oxdna_excv command :h3
-pair_style oxdna_stk command :h3
-pair_style oxdna_hbond command :h3
-pair_style oxdna_xstk command :h3
-pair_style oxdna_coaxstk command :h3
+pair_style oxdna/excv command :h3
+pair_style oxdna/stk command :h3
+pair_style oxdna/hbond command :h3
+pair_style oxdna/xstk command :h3
+pair_style oxdna/coaxstk command :h3
[Syntax:]
pair_style style :pre
-style = {hybrid/overlay oxdna_excv oxdna_stk oxdna_hbond oxdna_xstk oxdna_coaxstk} :ul
+style = {hybrid/overlay oxdna/excv oxdna/stk oxdna/hbond oxdna/xstk oxdna/coaxstk} :ul
[Examples:]
-pair_style hybrid/overlay oxdna_excv oxdna_stk oxdna_hbond oxdna_xstk oxdna_coaxstk
-pair_coeff * * oxdna_excv 2.0 0.7 0.675 2.0 0.515 0.5 2.0 0.33 0.32
-pair_coeff * * oxdna_stk 1.61048 6.0 0.4 0.9 0.32 0.6 1.3 0 0.8 0.9 0 0.95 0.9 0 0.95 2.0 0.65 2.0 0.65
-pair_coeff * * oxdna_hbond 0.0 8.0 0.4 0.75 0.34 0.7 1.5 0 0.7 1.5 0 0.7 1.5 0 0.7 0.46 3.141592653589793 0.7 4.0 1.5707963267948966 0.45 4.0 1.5707963267948966 0.45
-pair_coeff 1 4 oxdna_hbond 1.077 8.0 0.4 0.75 0.34 0.7 1.5 0 0.7 1.5 0 0.7 1.5 0 0.7 0.46 3.141592653589793 0.7 4.0 1.5707963267948966 0.45 4.0 1.5707963267948966 0.45
-pair_coeff 2 3 oxdna_hbond 1.077 8.0 0.4 0.75 0.34 0.7 1.5 0 0.7 1.5 0 0.7 1.5 0 0.7 0.46 3.141592653589793 0.7 4.0 1.5707963267948966 0.45 4.0 1.5707963267948966 0.45
-pair_coeff * * oxdna_xstk 47.5 0.575 0.675 0.495 0.655 2.25 0.791592653589793 0.58 1.7 1.0 0.68 1.7 1.0 0.68 1.5 0 0.65 1.7 0.875 0.68 1.7 0.875 0.68
-pair_coeff * * oxdna_coaxstk 46.0 0.4 0.6 0.22 0.58 2.0 2.541592653589793 0.65 1.3 0 0.8 0.9 0 0.95 0.9 0 0.95 2.0 -0.65 2.0 -0.65 :pre
+pair_style hybrid/overlay oxdna/excv oxdna/stk oxdna/hbond oxdna/xstk oxdna/coaxstk
+pair_coeff * * oxdna/excv 2.0 0.7 0.675 2.0 0.515 0.5 2.0 0.33 0.32
+pair_coeff * * oxdna/stk 1.61048 6.0 0.4 0.9 0.32 0.6 1.3 0 0.8 0.9 0 0.95 0.9 0 0.95 2.0 0.65 2.0 0.65
+pair_coeff * * oxdna/hbond 0.0 8.0 0.4 0.75 0.34 0.7 1.5 0 0.7 1.5 0 0.7 1.5 0 0.7 0.46 3.141592653589793 0.7 4.0 1.5707963267948966 0.45 4.0 1.5707963267948966 0.45
+pair_coeff 1 4 oxdna/hbond 1.077 8.0 0.4 0.75 0.34 0.7 1.5 0 0.7 1.5 0 0.7 1.5 0 0.7 0.46 3.141592653589793 0.7 4.0 1.5707963267948966 0.45 4.0 1.5707963267948966 0.45
+pair_coeff 2 3 oxdna/hbond 1.077 8.0 0.4 0.75 0.34 0.7 1.5 0 0.7 1.5 0 0.7 1.5 0 0.7 0.46 3.141592653589793 0.7 4.0 1.5707963267948966 0.45 4.0 1.5707963267948966 0.45
+pair_coeff * * oxdna/xstk 47.5 0.575 0.675 0.495 0.655 2.25 0.791592653589793 0.58 1.7 1.0 0.68 1.7 1.0 0.68 1.5 0 0.65 1.7 0.875 0.68 1.7 0.875 0.68
+pair_coeff * * oxdna/coaxstk 46.0 0.4 0.6 0.22 0.58 2.0 2.541592653589793 0.65 1.3 0 0.8 0.9 0 0.95 0.9 0 0.95 2.0 -0.65 2.0 -0.65 :pre
[Description:]
The {oxdna} pair styles compute the pairwise-additive parts of the oxDNA force field
for coarse-grained modelling of DNA. The effective interaction between the nucleotides consists of potentials for the
-excluded volume interaction {oxdna_excv}, the stacking {oxdna_stk}, cross-stacking {oxdna_xstk}
-and coaxial stacking interaction {oxdna_coaxstk} as well
-as the hydrogen-bonding interaction {oxdna_hbond} between complementary pairs of nucleotides on
+excluded volume interaction {oxdna/excv}, the stacking {oxdna/stk}, cross-stacking {oxdna/xstk}
+and coaxial stacking interaction {oxdna/coaxstk} as well
+as the hydrogen-bonding interaction {oxdna/hbond} between complementary pairs of nucleotides on
opposite strands.
The exact functional form of the pair styles is rather complex, which manifests itself in the 144 coefficients
@@ -46,13 +46,13 @@ We refer to "(Ouldridge-DPhil)"_#Ouldridge-DPhil and "(Ouldridge)"_#Ouldridge
for a detailed description of the oxDNA force field.
NOTE: These pair styles have to be used together with the related oxDNA bond style
-{oxdna_fene} for the connectivity of the phosphate backbone (see also documentation of
-"bond_style oxdna_fene"_bond_oxdna_fene.html). The coefficients
+{oxdna/fene} for the connectivity of the phosphate backbone (see also documentation of
+"bond_style oxdna/fene"_bond_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/Â and /duplex2/.
+Example input and data files can be found in examples/USER/cgdna/examples/duplex1/Â 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.
@@ -67,7 +67,7 @@ LAMMPS"_Section_start.html#start_3 section for more info on packages.
[Related commands:]
-"bond_style oxdna_fene"_bond_oxdna_fene.html, "fix nve/dotc/langevin"_fix_nve_dotc_langevin.html, "pair_coeff"_pair_coeff.html
+"bond_style oxdna/fene"_bond_oxdna.html, "fix nve/dotc/langevin"_fix_nve_dotc_langevin.html, "pair_coeff"_pair_coeff.html
[Default:] none
diff --git a/doc/src/pairs.txt b/doc/src/pairs.txt
index 7c18623d11..0d6ddbb373 100644
--- a/doc/src/pairs.txt
+++ b/doc/src/pairs.txt
@@ -65,7 +65,7 @@ Pair Styles :h1
pair_nb3b_harmonic
pair_nm
pair_none
- pair_oxdna_excv
+ pair_oxdna
pair_peri
pair_polymorphic
pair_quip
--
GitLab