From 95877f75a2cbd2bb32e8e6d3f8f7c4e9a88eaa85 Mon Sep 17 00:00:00 2001 From: sjplimp Date: Tue, 29 Jul 2008 19:56:08 +0000 Subject: [PATCH] git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@2003 f3b2605a-c512-4ea7-a41b-209d697bcdaa --- doc/bond_fene.html | 4 ++++ doc/bond_fene.txt | 4 ++++ doc/bond_fene_expand.html | 4 ++++ doc/bond_fene_expand.txt | 4 ++++ doc/fix_bond_swap.html | 2 +- doc/fix_bond_swap.txt | 2 +- doc/special_bonds.html | 5 ++++- doc/special_bonds.txt | 5 ++++- 8 files changed, 26 insertions(+), 4 deletions(-) diff --git a/doc/bond_fene.html b/doc/bond_fene.html index 70eaad690f..49fe2823c6 100644 --- a/doc/bond_fene.html +++ b/doc/bond_fene.html @@ -48,6 +48,10 @@ or read_restart commands: "molecular" package (which it is by default). See the Making LAMMPS section for more info on packages.

+

You typically should specify special_bonds 0 1 1 +to use this bond style. LAMMPS will issue a warning it that's not the +case. +

Related commands:

bond_coeff, delete_bonds diff --git a/doc/bond_fene.txt b/doc/bond_fene.txt index 6b2b2d2a4a..78f399e8fd 100644 --- a/doc/bond_fene.txt +++ b/doc/bond_fene.txt @@ -45,6 +45,10 @@ This bond style can only be used if LAMMPS was built with the "molecular" package (which it is by default). See the "Making LAMMPS"_Section_start.html#2_3 section for more info on packages. +You typically should specify "special_bonds 0 1 1"_special_bonds.html +to use this bond style. LAMMPS will issue a warning it that's not the +case. + [Related commands:] "bond_coeff"_bond_coeff.html, "delete_bonds"_delete_bonds.html diff --git a/doc/bond_fene_expand.html b/doc/bond_fene_expand.html index a122517286..586f9b91e5 100644 --- a/doc/bond_fene_expand.html +++ b/doc/bond_fene_expand.html @@ -53,6 +53,10 @@ or read_restart commands: "molecular" package (which it is by default). See the Making LAMMPS section for more info on packages.

+

You typically should specify special_bonds 0 1 1 +to use this bond style. LAMMPS will issue a warning it that's not the +case. +

Related commands:

bond_coeff, delete_bonds diff --git a/doc/bond_fene_expand.txt b/doc/bond_fene_expand.txt index e84623fba4..142766ff86 100644 --- a/doc/bond_fene_expand.txt +++ b/doc/bond_fene_expand.txt @@ -50,6 +50,10 @@ This bond style can only be used if LAMMPS was built with the "molecular" package (which it is by default). See the "Making LAMMPS"_Section_start.html#2_3 section for more info on packages. +You typically should specify "special_bonds 0 1 1"_special_bonds.html +to use this bond style. LAMMPS will issue a warning it that's not the +case. + [Related commands:] "bond_coeff"_bond_coeff.html, "delete_bonds"_delete_bonds.html diff --git a/doc/fix_bond_swap.html b/doc/fix_bond_swap.html index e0fe318532..96c198ca65 100644 --- a/doc/fix_bond_swap.html +++ b/doc/fix_bond_swap.html @@ -23,7 +23,7 @@

Examples:

-
fix 1 all bond/swap 0.5 1.5 598934 
+
fix 1 all bond/swap 0.5 1.3 598934 
 

 
Description:
 

diff --git a/doc/fix_bond_swap.txt b/doc/fix_bond_swap.txt
index fb796e715b..ed906b61b5 100755
--- a/doc/fix_bond_swap.txt
+++ b/doc/fix_bond_swap.txt
@@ -20,7 +20,7 @@ seed = random # seed (positive integer) :ul
 
 [Examples:]
 
-fix 1 all bond/swap 0.5 1.5 598934 :pre
+fix 1 all bond/swap 0.5 1.3 598934 :pre
 
 [Description:]
 
diff --git a/doc/special_bonds.html b/doc/special_bonds.html
index a3f5ac0b86..824a3d4132 100644
--- a/doc/special_bonds.html
+++ b/doc/special_bonds.html
@@ -24,7 +24,7 @@ special_bonds c1 c2 c3 c4 c5 c6
 

 
special_bonds charmm
 special_bonds amber
-special_bonds 0.0 0.0 1.0
+special_bonds 0 1 1
 special_bonds 0.0 0.0 1.0 0.0 0.0 0.5 
 

 
Description:
@@ -65,6 +65,9 @@ interactions and to 0.0 0.0 0.833 for Coulombic interactions, which is
 the default for a particular version of the AMBER force field, where
 the last value is 5/6.
 

+
For a lj units system with FENE bonds a
+setting of special bonds 0 1 1 should be used.
+

 
A special_bonds command with 3 coefficients sets the 1-2, 1-3, and 1-4
 coefficients for both LJ and Coulombic terms to those values.
 

diff --git a/doc/special_bonds.txt b/doc/special_bonds.txt
index b7e5dd24f7..548df8c7fc 100644
--- a/doc/special_bonds.txt
+++ b/doc/special_bonds.txt
@@ -21,7 +21,7 @@ Examples:
 
 special_bonds charmm
 special_bonds amber
-special_bonds 0.0 0.0 1.0
+special_bonds 0 1 1
 special_bonds 0.0 0.0 1.0 0.0 0.0 0.5 :pre
 
 [Description:]
@@ -62,6 +62,9 @@ interactions and to 0.0 0.0 0.833 for Coulombic interactions, which is
 the default for a particular version of the AMBER force field, where
 the last value is 5/6.
 
+For a "lj units"_units.html system with "FENE bonds"_bond_fene.html a
+setting of special bonds 0 1 1 should be used.
+
 A special_bonds command with 3 coefficients sets the 1-2, 1-3, and 1-4
 coefficients for both LJ and Coulombic terms to those values.