git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@4912 f3b2605a-c512-4ea7-a41b-209d697bcdaa

doc/fix_neb.html

@@ -13,11 +13,11 @@
 </H3>
 <P><B>Syntax:</B>
 </P>
-<PRE>fix ID group-ID neb kspring 
+<PRE>fix ID group-ID neb Kspring 
 </PRE>
 <UL><LI>ID, group-ID are documented in <A HREF = "fix.html">fix</A> command
 <LI>neb = style name of this fix command
-<LI>kspring = inter-replica spring constant 
+<LI>Kspring = inter-replica spring constant (force/distance units) 
 </UL>
 <P><B>Examples:</B>
 </P>
@@ -25,17 +25,20 @@
 </PRE>
 <P><B>Description:</B>
 </P>
-<P>Add inter-replica forces to atoms in the group for a multi-partition
+<P>Add inter-replica forces to atoms in the group for a multi-replica
 simulation run via the <A HREF = "neb.html">neb</A> command to perform a nudged
 elastic band (NEB) calculation for transition state finding.  Hi-level
 explanations of NEB are given with the <A HREF = "neb.html">neb</A> command and in
-<A HREF = "Section_howto.html#neb">this section</A> of the doc pages.  The fix neb
+<A HREF = "Section_howto.html#4_5">this section</A> of the manual.  The fix neb
-command is used to define how inter-replica forces are computed.
+command must be used with the "neb" command to define how
+inter-replica forces are computed.
 </P>
-<P>Atoms in the two end-point replicas do not experience inter-replica
+<P>Only the N atoms in the fix group experience inter-replica forces.
-forces, but those in intermediate replicas do.  The 3N-length vector
+Atoms in the two end-point replicas do not experience these forces,
-of interatomic forces Fi = -Grad(V) acting on the atoms of each
+but those in intermediate replicas do.  During the initial stage of
-intermediate replica I is altered to become:
+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 <A HREF = "#Henkelman1">(Henkelman1)</A> paper, to become:
 </P>
 <PRE>Fi = -Grad(V) + (Grad(V) dot That) That + Kspring (|Ri+i - Ri| - |Ri - Ri-1|) That 
 </PRE>
@@ -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
+roughly in the direction of (Ri+i - Ri-1); see the
-above equation are the component of the interatomic forces
+<A HREF = "#Henkelman1">(Henkelman1)</A> paper for details.
-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.
 </P>
-<P>NOTE: That is defined in what papers?
+<P>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 <I>Kspring</I>.
 </P>
 <P>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
@@ -62,20 +65,17 @@ parallel to the MEP itself.
 neighbors in a direction along the MEP, so that the final set of
 states are equidistant from each other.
 </P>
-<P>A NEB calculation is performed in two stages, as described by the neb
+<P>During the second stage of NEB, the forces on the N atoms in the
-command.  In the second stage, the forces on atoms in the replica
+replica nearest the top of the energy barrier are altered so that it
-nearest the top of the energy barrier are altered so that it climbs to
+climbs to the top of the barrier and finds the saddle point.  The
-the top of the barrier and finds the saddle point.  The forces on
+forces on atoms in this replica are described in the
-atoms in this replica become:
+<A HREF = "#Henkelman2">(Henkelman2)</A> paper, and become:
 </P>
-<PRE>Fi = -Grad(V) + 2 (Grad(V) dot that) that 
+<PRE>Fi = -Grad(V) + 2 (Grad(V) dot That) That 
 </PRE>
 <P>The inter-replica forces for the other replicas are unchanged from the
 first equation.
 </P>
-<P>NOTE: discuss how to do NEB on a subset of atoms - group ID of fix neb
-command.
-</P>
 <P><B>Restart, fix_modify, output, run start/stop, minimize info:</B>
 </P>
 <P>No information about this fix is written to <A HREF = "restart.html">binary restart
@@ -84,7 +84,10 @@ are relevant to this fix.  No global or per-atom quantities are stored
 by this fix for access by various <A HREF = "Section_howto.html#4_15">output
 commands</A>.  No parameter of this fix can be
 used with the <I>start/stop</I> keywords of the <A HREF = "run.html">run</A> command.
-This fix is not invoked during <A HREF = "minimize.html">energy minimization</A>.
+</P>
+<P>The forces due to this fix are imposed during an energy minimization,
+as invoked by the <A HREF = "minimize.html">minimize</A> command via the
+<A HREF = "neb.html">neb</A> command.
 </P>
 <P><B>Restrictions:</B>
 </P>
@@ -98,12 +101,13 @@ more info on packages.
 </P>
 <P><B>Default:</B> none
 </P>
-<A NAME = "HJ1"></A>
+<A NAME = "Henkelman"></A>
 
-<P><B>(Henkelman1)</B> Henkelman and Jonsson, J Phys Chem, 113, 9978-9985 (2000).
+<P><B>(Henkelman1)</B> Henkelman and Jonsson, J Chem Phys, 113, 9978-9985 (2000).
 </P>
-<A NAME = "HJ2"></A>
+<A NAME = "Henkelman"></A>
 
-<P><B>(Henkelman2)</B> Henkelman and Jonsson, J Phys Chem, 113, 99019904 (2000).
+<P><B>(Henkelman2)</B> Henkelman, Uberuaga, Jonsson, J Chem Phys, 113,
+9901-9904 (2000).
 </P>
 </HTML>

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
+"this section"_Section_howto.html#4_5 of the manual.  The fix neb
-command is used to define how inter-replica forces are computed.
+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
+Only the N atoms in the fix group experience inter-replica forces.
-forces, but those in intermediate replicas do.  The 3N-length vector
+Atoms in the two end-point replicas do not experience these forces,
-of interatomic forces Fi = -Grad(V) acting on the atoms of each
+but those in intermediate replicas do.  During the initial stage of
-intermediate replica I is altered to become:
+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
+roughly in the direction of (Ri+i - Ri-1); see the
-above equation are the component of the interatomic forces
+"(Henkelman1)"_#Henkelman1 paper for details.
-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.
 
-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
@@ -59,20 +62,17 @@ 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
+During the second stage of NEB, the forces on the N atoms in the
-command.  In the second stage, the forces on atoms in the replica
+replica nearest the top of the energy barrier are altered so that it
-nearest the top of the energy barrier are altered so that it climbs to
+climbs to the top of the barrier and finds the saddle point.  The
-the top of the barrier and finds the saddle point.  The forces on
+forces on atoms in this replica are described in the
-atoms in this replica become:
+"(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.
-
 [Restart, fix_modify, output, run start/stop, minimize info:]
 
 No information about this fix is written to "binary restart
@@ -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)
+:link(Henkelman)
-[(Henkelman1)] Henkelman and Jonsson, J Phys Chem, 113, 9978-9985 (2000).
+[(Henkelman1)] Henkelman and Jonsson, J Chem Phys, 113, 9978-9985 (2000).
 
-:link(HJ2)
+:link(Henkelman)
-[(Henkelman2)] Henkelman and Jonsson, J Phys Chem, 113, 99019904 (2000).
+[(Henkelman2)] Henkelman, Uberuaga, Jonsson, J Chem Phys, 113,
+9901-9904 (2000).

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 <I>dmax</I> 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 <A HREF = "units.html">units</A> means no atom will move
+For the <I>quickmin</I> and <I>fire</I> minimization styles, the <I>dmax</I> setting
+is how far any atom can move in a single iteration (timestep).  Thus a
+value of 0.1 in real <A HREF = "units.html">units</A> 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.

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.

doc/min_style.html

@@ -15,12 +15,12 @@
 </P>
 <PRE>min_style style 
 </PRE>
-<UL><LI>style = <I>cg</I> or <I>hftn</I> or <I>sd</I> 
+<UL><LI>style = <I>cg</I> or <I>hftn</I> or <I>sd</I> or <I>quickmin</I> or <I>fire</I> 
 </UL>
 <P><B>Examples:</B>
 </P>
 <PRE>min_style cg
-min_style hftn 
+min_style fire 
 </PRE>
 <P><B>Description:</B>
 </P>
@@ -33,7 +33,7 @@ previous iteration information to compute a new search direction
 perpendicular (conjugate) to the previous search direction.  The PR
 variant affects how the direction is chosen and how the CG method is
 restarted when it ceases to make progress.  The PR variant is thought
-to be the most effective CG choice.
+to be the most effective CG choice for most problems.
 </P>
 <P>Style <I>hftn</I> is a Hessian-free truncated Newton algorithm.  At each
 iteration a quadratic model of the energy potential is solved by a
@@ -43,9 +43,8 @@ conjugate search direction by a finite difference directional
 derivative.  When close to an energy minimum, the algorithm behaves
 like a Newton method and exhibits a quadratic convergence rate to high
 accuracy.  In most cases the behavior of <I>hftn</I> is similar to <I>cg</I>,
-but it offers another minimizer alternative if <I>cg</I> seems to perform
+but it offers an alternative if <I>cg</I> seems to perform poorly.  This
-poorly.  This style is not affected by the
+style is not affected by the <A HREF = "min_modify.html">min_modify</A> command.
-<A HREF = "min_modify.html">min_modify</A> command.
 </P>
 <P>Style <I>sd</I> is a steepest descent algorithm.  At each iteration, the
 search direction is set to the downhill direction corresponding to the
@@ -53,14 +52,45 @@ force vector (negative gradient of energy).  Typically, steepest
 descent will not converge as quickly as CG, but may be more robust in
 some situations.
 </P>
+<P>Style <I>quickmin</I> is a damped dynamics method described in
+<A HREF = "#Sheppard">(Sheppard)</A>, where the damping parameter is related to the
+projection of the velocity vector along the current force vector for
+each atom.
+</P>
+<P>Style <I>fire</I> is a damped dynamics method described in
+<A HREF = "#Bitzek">(Bitzek)</A>, which is similar to <I>quickmin</I> but adds a variable
+timestep and alters the projection operation to maintain components of
+the velocity non-parallel to the current force vector.
+</P>
+<P>Either the <I>quickmin</I> and <I>fire</I> styles are useful in the context of
+nudged elastic band (NEB</I> calculations via the <A HREF = "neb.html">neb</A> command.
+</P>
+<P>IMPORTANT NOTE: The <I>quickmin</I> and <I>fire</I> styles do not yet support
+the use of the <A HREF = "fix_box_relax.html">fix box/relax</A> command or
+minimizations involving the electron radius in <A HREF = "pair_eff.html">eFF</A>
+models.
+</P>
 <P><B>Restrictions:</B> none
 </P>
 <P><B>Related commands:</B>
 </P>
-<P><A HREF = "min_modify.html">min_modify</A>, <A HREF = "minimize.html">minimize</A>
+<P><A HREF = "min_modify.html">min_modify</A>, <A HREF = "minimize.html">minimize</A>, <A HREF = "neb.html">neb</A>
 </P>
 <P><B>Default:</B>
 </P>
 <PRE>min_style cg 
 </PRE>
+<HR>
+
+<A NAME = "Sheppard"></A>
+
+<P><B>(Sheppard)</B> Sheppard, Terrell, Henkelman, J Chem Phys, 128, 134106
+(2008).  See ref 1 in this paper for original reference to Qmin in
+Jonsson, Mills, Jacobsen.
+</P>
+<A NAME = "Bitzek"></A>
+
+<P><B><I>Bitzek</I></B> Bitzek, Koskinen, Gahler, Moseler, Gumbsch, Phys Rev Lett,
+97, 170201 (2006).
+</P>
 </HTML>

doc/min_style.txt

@@ -11,12 +11,12 @@ min_style command :h3
 
 min_style style :pre
 
-style = {cg} or {hftn} or {sd} :ul
+style = {cg} or {hftn} or {sd} or {quickmin} or {fire} :ul
 
 [Examples:]
 
 min_style cg
-min_style hftn :pre
+min_style fire :pre
 
 [Description:]
 
@@ -29,7 +29,7 @@ previous iteration information to compute a new search direction
 perpendicular (conjugate) to the previous search direction.  The PR
 variant affects how the direction is chosen and how the CG method is
 restarted when it ceases to make progress.  The PR variant is thought
-to be the most effective CG choice.
+to be the most effective CG choice for most problems.
 
 Style {hftn} is a Hessian-free truncated Newton algorithm.  At each
 iteration a quadratic model of the energy potential is solved by a
@@ -39,9 +39,8 @@ conjugate search direction by a finite difference directional
 derivative.  When close to an energy minimum, the algorithm behaves
 like a Newton method and exhibits a quadratic convergence rate to high
 accuracy.  In most cases the behavior of {hftn} is similar to {cg},
-but it offers another minimizer alternative if {cg} seems to perform
+but it offers an alternative if {cg} seems to perform poorly.  This
-poorly.  This style is not affected by the
+style is not affected by the "min_modify"_min_modify.html command.
-"min_modify"_min_modify.html command.
 
 Style {sd} is a steepest descent algorithm.  At each iteration, the
 search direction is set to the downhill direction corresponding to the
@@ -49,12 +48,42 @@ force vector (negative gradient of energy).  Typically, steepest
 descent will not converge as quickly as CG, but may be more robust in
 some situations.
 
+Style {quickmin} is a damped dynamics method described in
+"(Sheppard)"_#Sheppard, where the damping parameter is related to the
+projection of the velocity vector along the current force vector for
+each atom.
+
+Style {fire} is a damped dynamics method described in
+"(Bitzek)"_#Bitzek, which is similar to {quickmin} but adds a variable
+timestep and alters the projection operation to maintain components of
+the velocity non-parallel to the current force vector.
+
+Either the {quickmin} and {fire} styles are useful in the context of
+nudged elastic band (NEB} calculations via the "neb"_neb.html command.
+
+IMPORTANT NOTE: The {quickmin} and {fire} styles do not yet support
+the use of the "fix box/relax"_fix_box_relax.html command or
+minimizations involving the electron radius in "eFF"_pair_eff.html
+models.
+
 [Restrictions:] none
 
 [Related commands:]
 
-"min_modify"_min_modify.html, "minimize"_minimize.html
+"min_modify"_min_modify.html, "minimize"_minimize.html, "neb"_neb.html
 
 [Default:]
 
 min_style cg :pre
+
+:line
+
+:link(Sheppard)
+[(Sheppard)] Sheppard, Terrell, Henkelman, J Chem Phys, 128, 134106
+(2008).  See ref 1 in this paper for original reference to Qmin in
+Jonsson, Mills, Jacobsen.
+
+:link(Bitzek)
+[{Bitzek}] Bitzek, Koskinen, Gahler, Moseler, Gumbsch, Phys Rev Lett,
+97, 170201 (2006).
+

doc/minimize.html

@@ -50,15 +50,21 @@ slowly drains all kinetic energy from the system.  The <A HREF = "pair_soft.html
 soft</A> potential can be used to un-overlap atoms while
 running dynamics.
 </P>
-<P>A minimization involves an outer iteration loop which sets the search
+<P>The <A HREF = "min_style.html">minimization styles</A> <I>cg</I>, <I>sd</I>, and <I>hftn</I>
-direction along which atom coordinates are changed.  An inner
+involves an outer iteration loop which sets the search direction along
-iteration is then performed using a line search algorithm.  The line
+which atom coordinates are changed.  An inner iteration is then
-search typically evaluates forces and energies several times to set
+performed using a line search algorithm.  The line search typically
-new coordinates.  Currently, a backtracking algorithm is used which
+evaluates forces and energies several times to set new coordinates.
-may not be optimal in terms of the number of force evaulations
+Currently, a backtracking algorithm is used which may not be optimal
-performed, but appears to be more robust than previous line searches
+in terms of the number of force evaulations performed, but appears to
-we've tried.  The backtracking method is described in Nocedal and
+be more robust than previous line searches we've tried.  The
-Wright's Numerical Optimization (Procedure 3.1 on p 41).
+backtracking method is described in Nocedal and Wright's Numerical
+Optimization (Procedure 3.1 on p 41).
+</P>
+<P>The <A HREF = "min_style.html">minimization styles</A> <I>quickmin</I> and <I>fire</I> perform
+damped dynamics using an Euler integration step.  Thus they require a
+<A HREF = "timestep.html">timestep</A> be defined, typically the same value used for
+<A HREF = "run.html">running dynamics</A> with the system.
 </P>
 <P>The objective function being minimized is the total potential energy
 of the system as a function of the N atom coordinates:
@@ -85,7 +91,7 @@ of the atoms.
 <UL><LI>the change in energy between outer iterations is less than <I>etol</I>
 <LI>the 2-norm (length) of the global force vector is less than the <I>ftol</I>
 <LI>the line search fails because the step distance backtracks to 0.0
-<LI>the number of outer iterations exceeds <I>maxiter</I>
+<LI>the number of outer iterations or timesteps exceeds <I>maxiter</I>
 <LI>the number of total force evaluations exceeds <I>maxeval</I> 
 </UL>
 <P>For the first criterion, the specified energy tolerance <I>etol</I> is

doc/minimize.txt

@@ -47,15 +47,21 @@ slowly drains all kinetic energy from the system.  The "pair_style
 soft"_pair_soft.html potential can be used to un-overlap atoms while
 running dynamics.
 
-A minimization involves an outer iteration loop which sets the search
+The "minimization styles"_min_style.html {cg}, {sd}, and {hftn}
-direction along which atom coordinates are changed.  An inner
+involves an outer iteration loop which sets the search direction along
-iteration is then performed using a line search algorithm.  The line
+which atom coordinates are changed.  An inner iteration is then
-search typically evaluates forces and energies several times to set
+performed using a line search algorithm.  The line search typically
-new coordinates.  Currently, a backtracking algorithm is used which
+evaluates forces and energies several times to set new coordinates.
-may not be optimal in terms of the number of force evaulations
+Currently, a backtracking algorithm is used which may not be optimal
-performed, but appears to be more robust than previous line searches
+in terms of the number of force evaulations performed, but appears to
-we've tried.  The backtracking method is described in Nocedal and
+be more robust than previous line searches we've tried.  The
-Wright's Numerical Optimization (Procedure 3.1 on p 41).
+backtracking method is described in Nocedal and Wright's Numerical
+Optimization (Procedure 3.1 on p 41).
+
+The "minimization styles"_min_style.html {quickmin} and {fire} perform
+damped dynamics using an Euler integration step.  Thus they require a
+"timestep"_timestep.html be defined, typically the same value used for
+"running dynamics"_run.html with the system.
 
 The objective function being minimized is the total potential energy
 of the system as a function of the N atom coordinates:
@@ -82,7 +88,7 @@ The minimization procedure stops if any of several criteria are met:
 the change in energy between outer iterations is less than {etol}
 the 2-norm (length) of the global force vector is less than the {ftol}
 the line search fails because the step distance backtracks to 0.0
-the number of outer iterations exceeds {maxiter}
+the number of outer iterations or timesteps exceeds {maxiter}
 the number of total force evaluations exceeds {maxeval} :ul
 
 For the first criterion, the specified energy tolerance {etol} is

doc/neb.html

@@ -264,11 +264,11 @@ langevin</A>, <A HREF = "fix_viscous.html">fix viscous</A>
 
 <A NAME = "Henkelman1"></A>
 
-<P><B>(Henkelman1)</B> Henkelman and Jonsson, J Phys Chem, 113, 9978-9985 (2000).
+<P><B>(Henkelman1)</B> Henkelman and Jonsson, J Chem Phys, 113, 9978-9985 (2000).
 </P>
 <A NAME = "Henkelman2"></A>
 
-<P><B>(Henkelman2)</B> Henkelman, Uberuaga, Jonsson, J Phys Chem, 113,
+<P><B>(Henkelman2)</B> Henkelman, Uberuaga, Jonsson, J Chem Phys, 113,
 9901-9904 (2000).
 </P>
 <A NAME = "Nakano"></A>

doc/neb.txt

@@ -260,10 +260,10 @@ langevin"_fix_langevin.html, "fix viscous"_fix_viscous.html
 :line
 
 :link(Henkelman1)
-[(Henkelman1)] Henkelman and Jonsson, J Phys Chem, 113, 9978-9985 (2000).
+[(Henkelman1)] Henkelman and Jonsson, J Chem Phys, 113, 9978-9985 (2000).
 
 :link(Henkelman2)
-[(Henkelman2)] Henkelman, Uberuaga, Jonsson, J Phys Chem, 113,
+[(Henkelman2)] Henkelman, Uberuaga, Jonsson, J Chem Phys, 113,
 9901-9904 (2000).
 
 :link(Nakano)