diff --git a/doc/fix_neb.html b/doc/fix_neb.html index 0a8c2584b0..69837ca052 100644 --- a/doc/fix_neb.html +++ b/doc/fix_neb.html @@ -13,11 +13,11 @@

Syntax:

-
fix ID group-ID neb kspring 
+
fix ID group-ID neb Kspring 
 

 
 
Examples:
 

@@ -25,17 +25,20 @@

Description:

-

Add inter-replica forces to atoms in the group for a multi-partition +

Add inter-replica forces to atoms in the group for a multi-replica simulation run via the neb command to perform a nudged elastic band (NEB) calculation for transition state finding. Hi-level explanations of NEB are given with the neb command and in -this section of the doc pages. The fix neb -command is used to define how inter-replica forces are computed. +this section of the manual. The fix neb +command must be used with the "neb" command to define how +inter-replica forces are computed.

-

Atoms in the two end-point replicas do not experience inter-replica -forces, but those in intermediate replicas do. The 3N-length vector -of interatomic forces Fi = -Grad(V) acting on the atoms of each -intermediate replica I is altered to become: +

Only the N atoms in the fix group experience inter-replica forces. +Atoms in the two end-point replicas do not experience these forces, +but those in intermediate replicas do. During the initial stage of +NEB, the 3N-length vector of interatomic forces Fi = -Grad(V) acting +on the atoms of each intermediate replica I is altered, as described +in the (Henkelman1) paper, to become: 

Fi = -Grad(V) + (Grad(V) dot That) That + Kspring (|Ri+i - Ri| - |Ri - Ri-1|) That
@@ -43,13 +46,13 @@ intermediate replica I is altered to become: coordinates of its neighbor replicas. That (t with a hat over it) is the unit "tangent" vector for replica I which is a function of Ri, Ri-1, Ri+1, and the potential energy of the 3 replicas; it points -roughly in the direction of (Ri+i - Ri-1). The first two terms in the -above equation are the component of the interatomic forces -perpendicular to the tangent vector. The last term is a spring force -between replica I and its neighbors, parallel to the tangent vector -direction with the specified spring constant. +roughly in the direction of (Ri+i - Ri-1); see the +(Henkelman1) paper for details.

-

NOTE: That is defined in what papers? +

The first two terms in the above equation are the component of the +interatomic forces perpendicular to the tangent vector. The last term +is a spring force between replica I and its neighbors, parallel to the +tangent vector direction with the specified spring constant Kspring.

The effect of the first two terms is to push the atoms of each replica toward the minimum energy path (MEP) of conformational states that @@ -62,19 +65,16 @@ parallel to the MEP itself. neighbors in a direction along the MEP, so that the final set of states are equidistant from each other.

-

A NEB calculation is performed in two stages, as described by the neb -command. In the second stage, the forces on atoms in the replica -nearest the top of the energy barrier are altered so that it climbs to -the top of the barrier and finds the saddle point. The forces on -atoms in this replica become: +

During the second stage of NEB, the forces on the N atoms in the +replica nearest the top of the energy barrier are altered so that it +climbs to the top of the barrier and finds the saddle point. The +forces on atoms in this replica are described in the +(Henkelman2) paper, and become:

-
Fi = -Grad(V) + 2 (Grad(V) dot that) that 
+
Fi = -Grad(V) + 2 (Grad(V) dot That) That 
 

 
The inter-replica forces for the other replicas are unchanged from the
-first equation. 
-

-
NOTE: discuss how to do NEB on a subset of atoms - group ID of fix neb
-command.
+first equation.
 

 
Restart, fix_modify, output, run start/stop, minimize info:
 

@@ -84,7 +84,10 @@ are relevant to this fix.  No global or per-atom quantities are stored
 by this fix for access by various output
 commands.  No parameter of this fix can be
 used with the start/stop keywords of the run command.
-This fix is not invoked during energy minimization.
+

+
The forces due to this fix are imposed during an energy minimization,
+as invoked by the minimize command via the
+neb command.
 

 
Restrictions:
 

@@ -98,12 +101,13 @@ more info on packages.
 

 
Default: none
 

-
+
 
-
(Henkelman1) Henkelman and Jonsson, J Phys Chem, 113, 9978-9985 (2000).
+
(Henkelman1) Henkelman and Jonsson, J Chem Phys, 113, 9978-9985 (2000).
 

-
+
 
-
(Henkelman2) Henkelman and Jonsson, J Phys Chem, 113, 99019904 (2000).
+
(Henkelman2) Henkelman, Uberuaga, Jonsson, J Chem Phys, 113,
+9901-9904 (2000).
 

 
diff --git a/doc/fix_neb.txt b/doc/fix_neb.txt
index c488aaed8b..353bde8bfd 100644
--- a/doc/fix_neb.txt
+++ b/doc/fix_neb.txt
@@ -10,11 +10,11 @@ fix neb command :h3
 
 [Syntax:]
 
-fix ID group-ID neb kspring :pre
+fix ID group-ID neb Kspring :pre
   
 ID, group-ID are documented in "fix"_fix.html command
 neb = style name of this fix command
-kspring = inter-replica spring constant :ul
+Kspring = inter-replica spring constant (force/distance units) :ul
 
 [Examples:]
 
@@ -22,17 +22,20 @@ fix 1 active neb 10.0 :pre
 
 [Description:]
 
-Add inter-replica forces to atoms in the group for a multi-partition
+Add inter-replica forces to atoms in the group for a multi-replica
 simulation run via the "neb"_neb.html command to perform a nudged
 elastic band (NEB) calculation for transition state finding.  Hi-level
 explanations of NEB are given with the "neb"_neb.html command and in
-"this section"_Section_howto.html#neb of the doc pages.  The fix neb
-command is used to define how inter-replica forces are computed.
+"this section"_Section_howto.html#4_5 of the manual.  The fix neb
+command must be used with the "neb" command to define how
+inter-replica forces are computed.
 
-Atoms in the two end-point replicas do not experience inter-replica
-forces, but those in intermediate replicas do.  The 3N-length vector
-of interatomic forces Fi = -Grad(V) acting on the atoms of each
-intermediate replica I is altered to become:
+Only the N atoms in the fix group experience inter-replica forces.
+Atoms in the two end-point replicas do not experience these forces,
+but those in intermediate replicas do.  During the initial stage of
+NEB, the 3N-length vector of interatomic forces Fi = -Grad(V) acting
+on the atoms of each intermediate replica I is altered, as described
+in the "(Henkelman1)"_#Henkelman1 paper, to become:
 
 Fi = -Grad(V) + (Grad(V) dot That) That + Kspring (|Ri+i - Ri| - |Ri - Ri-1|) That :pre
 
@@ -40,13 +43,13 @@ Ri are the atomic coordinates of replica I; Ri-1 and Ri+1 are the
 coordinates of its neighbor replicas.  That (t with a hat over it) is
 the unit "tangent" vector for replica I which is a function of Ri,
 Ri-1, Ri+1, and the potential energy of the 3 replicas; it points
-roughly in the direction of (Ri+i - Ri-1).  The first two terms in the
-above equation are the component of the interatomic forces
-perpendicular to the tangent vector.  The last term is a spring force
-between replica I and its neighbors, parallel to the tangent vector
-direction with the specified spring constant.
+roughly in the direction of (Ri+i - Ri-1); see the
+"(Henkelman1)"_#Henkelman1 paper for details.
 
-NOTE: That is defined in what papers?
+The first two terms in the above equation are the component of the
+interatomic forces perpendicular to the tangent vector.  The last term
+is a spring force between replica I and its neighbors, parallel to the
+tangent vector direction with the specified spring constant {Kspring}.
 
 The effect of the first two terms is to push the atoms of each replica
 toward the minimum energy path (MEP) of conformational states that
@@ -59,19 +62,16 @@ The effect of the last term is to push each replica away from its two
 neighbors in a direction along the MEP, so that the final set of
 states are equidistant from each other.
 
-A NEB calculation is performed in two stages, as described by the neb
-command.  In the second stage, the forces on atoms in the replica
-nearest the top of the energy barrier are altered so that it climbs to
-the top of the barrier and finds the saddle point.  The forces on
-atoms in this replica become:
+During the second stage of NEB, the forces on the N atoms in the
+replica nearest the top of the energy barrier are altered so that it
+climbs to the top of the barrier and finds the saddle point.  The
+forces on atoms in this replica are described in the
+"(Henkelman2)"_#Henkelman2 paper, and become:
 
-Fi = -Grad(V) + 2 (Grad(V) dot that) that :pre
+Fi = -Grad(V) + 2 (Grad(V) dot That) That :pre
 
 The inter-replica forces for the other replicas are unchanged from the
-first equation. 
-
-NOTE: discuss how to do NEB on a subset of atoms - group ID of fix neb
-command.
+first equation.
 
 [Restart, fix_modify, output, run start/stop, minimize info:]
 
@@ -81,7 +81,10 @@ are relevant to this fix.  No global or per-atom quantities are stored
 by this fix for access by various "output
 commands"_Section_howto.html#4_15.  No parameter of this fix can be
 used with the {start/stop} keywords of the "run"_run.html command.
-This fix is not invoked during "energy minimization"_minimize.html.
+
+The forces due to this fix are imposed during an energy minimization,
+as invoked by the "minimize"_minimize.html command via the
+"neb"_neb.html command.
 
 [Restrictions:]
 
@@ -95,8 +98,9 @@ more info on packages.
 
 [Default:] none
 
-:link(HJ1)
-[(Henkelman1)] Henkelman and Jonsson, J Phys Chem, 113, 9978-9985 (2000).
+:link(Henkelman)
+[(Henkelman1)] Henkelman and Jonsson, J Chem Phys, 113, 9978-9985 (2000).
 
-:link(HJ2)
-[(Henkelman2)] Henkelman and Jonsson, J Phys Chem, 113, 99019904 (2000).
+:link(Henkelman)
+[(Henkelman2)] Henkelman, Uberuaga, Jonsson, J Chem Phys, 113,
+9901-9904 (2000).
diff --git a/doc/min_modify.html b/doc/min_modify.html
index f22c4dc5d5..d93a9ad93f 100644
--- a/doc/min_modify.html
+++ b/doc/min_modify.html
@@ -41,7 +41,9 @@ with these parameters to tune their minimizations.
 inner iteration which is steps along a one-dimensional line search in
 a particular search direction.  The dmax parameter is how far any
 atom can move in a single line search in any dimension (x, y, or z).
-Thus a value of 0.1 in real units means no atom will move
+For the quickmin and fire minimization styles, the dmax setting
+is how far any atom can move in a single iteration (timestep).  Thus a
+value of 0.1 in real units means no atom will move
 further than 0.1 Angstroms in a single outer iteration.  This prevents
 highly overlapped atoms from being moved long distances (e.g. through
 another atom) due to large forces.
diff --git a/doc/min_modify.txt b/doc/min_modify.txt
index 7716c605cb..6e4306a3ac 100644
--- a/doc/min_modify.txt
+++ b/doc/min_modify.txt
@@ -36,7 +36,9 @@ The {cg} and {sd} minimization styles have an outer iteration and an
 inner iteration which is steps along a one-dimensional line search in
 a particular search direction.  The {dmax} parameter is how far any
 atom can move in a single line search in any dimension (x, y, or z).
-Thus a value of 0.1 in real "units"_units.html means no atom will move
+For the {quickmin} and {fire} minimization styles, the {dmax} setting
+is how far any atom can move in a single iteration (timestep).  Thus a
+value of 0.1 in real "units"_units.html means no atom will move
 further than 0.1 Angstroms in a single outer iteration.  This prevents
 highly overlapped atoms from being moved long distances (e.g. through
 another atom) due to large forces.
diff --git a/doc/min_style.html b/doc/min_style.html
index 7fe38f5a89..2e6fdc5da0 100644
--- a/doc/min_style.html
+++ b/doc/min_style.html
@@ -15,12 +15,12 @@
 

 
min_style style 
 

-