From 39bda1ee111cfe150c178797ad87f59e64c07ce4 Mon Sep 17 00:00:00 2001 From: sjplimp Date: Tue, 22 May 2012 13:56:16 +0000 Subject: [PATCH] git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@8119 f3b2605a-c512-4ea7-a41b-209d697bcdaa --- doc/fix_restrain.html | 44 +++++++++++++++++++++++++------------------ doc/fix_restrain.txt | 43 +++++++++++++++++++++++++----------------- 2 files changed, 52 insertions(+), 35 deletions(-) diff --git a/doc/fix_restrain.html b/doc/fix_restrain.html index d42f07cc09..fffc7fe3fe 100644 --- a/doc/fix_restrain.html +++ b/doc/fix_restrain.html @@ -13,43 +13,51 @@

Syntax:

-
fix ID group-ID restrain Kstart Kstop keyword value(s) 
+
fix ID group-ID restrain keyword args ... 
 

 
 
Examples:
 

-
fix holdem all restrain 2000.0 2000.0 dihedral 1 2 3 4 120.0
-fix texas_holdem all restrain 0.0 2000.0 dihedral 1 2 3 4 120.0 1 2 3 5 -120.0 1 2 3 6 0.0 
+
fix holdem all restrain bond 45 48 2000.0 2000.0 2.75
+fix holdem all restrain dihedral 1 2 3 4 2000.0 2000.0 120.0
+fix holdem all restrain bond 45 48 2000.0 2000.0 2.75 dihedral 1 2 3 4 2000.0 2000.0 120.0
+fix texas_holdem all restrain dihedral 1 2 3 4 0.0 2000.0 120.0 dihedral 1 2 3 5 0.0 2000.0 -120.0 dihedral 1 2 3 6 0.0 2000.0 0.0 
 

 
Description:
 

-
Restrain the motion of the specified atoms by making them part of a
-bond or angle or dihedral interaction whose strength can vary over
+
Restrain the motion of the specified sets of atoms by making them part
+of bond or angle or dihedral interaction whose strength can vary over
 time during a simulation.  This is functionally equivalent to creating
-a bond or angle or dihedral for the atoms in a data file, as specified
-by the read_data command, albeit with a time-varying
-pre-factor coefficient.  For the purpose of forcefield
+a bond or angle or dihedral for the same atoms in a data file, as
+specified by the read_data command, albeit with a
+time-varying pre-factor coefficient.  For the purpose of forcefield
 parameter-fitting or mapping a molecular potential energy surface,
 this fix reduces the hassle and risk associated with modifying data
 files.  In other words, use this fix to temporarily force a molecule
-to adopt a particular conformation. To form a permanent bond or angle
-or dihedral, modify the data file.
+to adopt a particular conformation.  To create a permanent bond or
+angle or dihedral, you should modify the data file.
 

 
The first example above applies a restraint to hold the dihedral angle
 formed by atoms 1, 2, 3, and 4 near 120 degrees using a constant
diff --git a/doc/fix_restrain.txt b/doc/fix_restrain.txt
index f70eded736..a34b5a7a77 100644
--- a/doc/fix_restrain.txt
+++ b/doc/fix_restrain.txt
@@ -10,37 +10,46 @@ fix restrain command :h3
 
 [Syntax:]
 
-fix ID group-ID restrain Kstart Kstop keyword value(s) :pre
+fix ID group-ID restrain keyword args ... :pre
 
 ID, group-ID are documented in "fix"_fix.html command :ulb,l
 restrain = style name of this fix command :l
-Kstart, Kstop = restraint coefficient at start/end of run (energy
-units) :l
-one keyword with one or more sets of parameter values may be appended to args :l
-keyword = {dihedral}  :l
-  {dihedral} value = atom1 atom2 atom3 atom4 target
-    atom1,atom2,atom3,atom4 = IDs of 4 atoms in restrained dihedral
-    target = target value for specified dihedral angle (degrees) :pre
+one or more keyword/arg pairs may be appended :l
+keyword = {bond} or {angle} or {dihedral} :l
+  {bond} args = atom1 atom2 Kstart Kstop r0
+    atom1,atom2 = IDs of 2 atoms in bond
+    Kstart,Kstop = restraint coefficients at start/end of run (energy units)
+    r0 = target value for bond distance (distance units)
+  {angle} args = atom1 atom2 atom3 Kstart Kstop theta
+    atom1,atom2,atom3 = IDs of 3 atoms in angle, atom2 = middle atom
+    Kstart,Kstop = restraint coefficients at start/end of run (energy units)
+    theta = target value for angle theta (degrees)
+  {bond} args = atom1 atom2 atom3 atom4 Kstart Kstop phi
+    atom1,atom2,atom3,atom4 = IDs of 4 atoms in dihedral in linear order
+    Kstart,Kstop = restraint coefficients at start/end of run (energy units)
+    phi = target value for dihedral angle phi (degrees) :pre
 :ule
 
 [Examples:]
 
-fix holdem all restrain 2000.0 2000.0 dihedral 1 2 3 4 120.0
-fix texas_holdem all restrain 0.0 2000.0 dihedral 1 2 3 4 120.0 1 2 3 5 -120.0 1 2 3 6 0.0 :pre
+fix holdem all restrain bond 45 48 2000.0 2000.0 2.75
+fix holdem all restrain dihedral 1 2 3 4 2000.0 2000.0 120.0
+fix holdem all restrain bond 45 48 2000.0 2000.0 2.75 dihedral 1 2 3 4 2000.0 2000.0 120.0
+fix texas_holdem all restrain dihedral 1 2 3 4 0.0 2000.0 120.0 dihedral 1 2 3 5 0.0 2000.0 -120.0 dihedral 1 2 3 6 0.0 2000.0 0.0 :pre
 
 [Description:]
 
-Restrain the motion of the specified atoms by making them part of a
-bond or angle or dihedral interaction whose strength can vary over
+Restrain the motion of the specified sets of atoms by making them part
+of bond or angle or dihedral interaction whose strength can vary over
 time during a simulation.  This is functionally equivalent to creating
-a bond or angle or dihedral for the atoms in a data file, as specified
-by the "read_data"_read_data.html command, albeit with a time-varying
-pre-factor coefficient.  For the purpose of forcefield
+a bond or angle or dihedral for the same atoms in a data file, as
+specified by the "read_data"_read_data.html command, albeit with a
+time-varying pre-factor coefficient.  For the purpose of forcefield
 parameter-fitting or mapping a molecular potential energy surface,
 this fix reduces the hassle and risk associated with modifying data
 files.  In other words, use this fix to temporarily force a molecule
-to adopt a particular conformation. To form a permanent bond or angle
-or dihedral, modify the data file.
+to adopt a particular conformation.  To create a permanent bond or
+angle or dihedral, you should modify the data file.
 
 The first example above applies a restraint to hold the dihedral angle
 formed by atoms 1, 2, 3, and 4 near 120 degrees using a constant