From a5110d81ea6133a74b79d5bf1be433a3d4625995 Mon Sep 17 00:00:00 2001
From: Axel Kohlmeyer <akohlmey@gmail.com>
Date: Fri, 19 May 2017 12:13:23 -0400
Subject: [PATCH] correct a bunch of documentation formatting issues for
 updated neb and fix neb commands

---
 doc/src/fix_neb.txt | 246 +++++++++--------
 doc/src/neb.txt     | 645 ++++++++++++++++++++++++--------------------
 2 files changed, 483 insertions(+), 408 deletions(-)

diff --git a/doc/src/fix_neb.txt b/doc/src/fix_neb.txt
index 0250a40d8c..a5c4bf4396 100644
--- a/doc/src/fix_neb.txt
+++ b/doc/src/fix_neb.txt
@@ -1,8 +1,8 @@
 "LAMMPS WWW Site"_lws - "LAMMPS Documentation"_ld - "LAMMPS Commands"_lc :c
 
-:link(lws,http://lammps.sandia.gov) 
+:link(lws,http://lammps.sandia.gov)
 :link(ld,Manual.html)
-
+:link(lc,Section_commands.html#comm)
 
 :line
 
@@ -11,164 +11,184 @@ fix neb command :h3
 [Syntax:]
 
 fix ID group-ID neb Kspring keyword value :pre
-  
-ID, group-ID are documented in "fix"_fix.html command neb = style name of this
-fix command Kspring = parallel spring constant (force/distance units) :ul
-keyword = {idealpos} or {neigh} or {perp} or {freeend} {idealpos} value = none =
-each replica is attached with a spring to its interpolated ideal position
-(default value) {neigh} value = none = each replica is attached with a spring
-with the previous and next replica.  {perp} value = spring constant for the
-perpendicular spring {freeend} value = ini or final or finaleini or final2eini
 
-  
+ID, group-ID are documented in "fix"_fix.html command
+neb = style name of this fix command
+Kspring = parallel spring constant (force/distance units)
+keyword = {idealpos} or {neigh} or {perp} or {freeend} :ul
+ {idealpos} = each replica is attached with a spring to its interpolated ideal position (default)
+ {neigh} = each replica is connected with spring to the previous and next replica.
+ {perp} value = set spring constant for the perpendicular spring to {value}
+ {freeend} flag = set behavior for the end points
+   flag = {ini} or {final} or {finaleini} or {final2eini}
+   :pre
 
 [Examples:]
 
-fix 1 active neb 10.0 :pre fix 2 all neb 1.0 perp 1.0 freeend final :pre fix 1
-all neb 1.0 neigh freeend final2eini :pre
+fix 1 active neb 10.0
+fix 2 all neb 1.0 perp 1.0 freeend final
+fix 1 all neb 1.0 neigh freeend final2eini :pre
 
 [Description:]
 
-Add a nudging force 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 finding the transition state.  Hi-level explanations of NEB are given with
-the "neb"_neb.html command and in "Section_howto 5"_Section_howto.html#howto_5
-of the manual.  The fix neb command must be used with the "neb" command and
-defines how nudging inter-replica forces are computed.  A NEB calculation is
-divided in two stages. In the first stage n replicas are relaxed toward a MEP
-and in a second stage, the climbing image scheme (see
-"(Henkelman2)"_#Henkelman2) is turned on so that the replica having the highest
-energy relaxes toward the saddle point (i.e. the point of highest energy along
-the MEP).
-
-One purpose of the nudging forces is to keep the replicas equally spaced.
-During the NEB, the 3N-length vector of interatomic force Fi = -Grad(V) of
-replicas i is altered. For all intermediate replicas (i.e. for 1<i<n) except for
-the climbing replica the force vector becomes:
+Add a nudging force 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 finding the transition state.
+Hi-level explanations of NEB are given with the "neb"_neb.html command
+and in "Section_howto 5"_Section_howto.html#howto_5 of the manual.
+The fix neb command must be used with the "neb" command and defines
+how nudging inter-replica forces are computed.  A NEB calculation is
+divided in two stages. In the first stage n replicas are relaxed
+toward a MEP and in a second stage, the climbing image scheme (see
+"(Henkelman2)"_#Henkelman2) is turned on so that the replica having
+the highest energy relaxes toward the saddle point (i.e. the point of
+highest energy along the MEP).
+
+One purpose of the nudging forces is to keep the replicas equally
+spaced.  During the NEB, the 3N-length vector of interatomic force Fi
+= -Grad(V) of replicas i is altered. For all intermediate replicas
+(i.e. for 1<i<n) except for the climbing replica the force vector
+becomes:
 
 Fi = -Grad(V) + (Grad(V) dot That) That + Fspringparallel + Fspringperp :pre
 
-That is the unit "tangent" vector for replica i and 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) (see the "(Henkelman1)"_#Henkelman1 paper for
-details).  Ri are the atomic coordinates of replica i; Ri-1 and Ri+1 are the
-coordinates of its neighbor replicas.  The term (Grad(V) dot That) is used to
-remove the component of the gradient parallel to the path which would tend to
+That is the unit "tangent" vector for replica i and 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) (see the
+"(Henkelman1)"_#Henkelman1 paper for details).  Ri are the atomic
+coordinates of replica i; Ri-1 and Ri+1 are the coordinates of its
+neighbor replicas.  The term (Grad(V) dot That) is used to remove the
+component of the gradient parallel to the path which would tend to
 distribute the replica unevenly along the path.  Fspringparallel is an
-artificial spring force which is applied only in the tangent direction and which
-maintains the replicas equally spaced (see below for more information).
-Fspringperp is an optinal artificial spring which is applied only perpendicular
-to the tangent and which prevent the paths from forming too acute kinks (see
-below for more information).
+artificial spring force which is applied only in the tangent direction
+and which maintains the replicas equally spaced (see below for more
+information).  Fspringperp is an optinal artificial spring which is
+applied only perpendicular to the tangent and which prevent the paths
+from forming too acute kinks (see below for more information).
 
 
-In the second stage of the NEB, the interatomic force Fi for the climbing
-replica (which is the replica of highest energy) becomes :
+In the second stage of the NEB, the interatomic force Fi for the
+climbing replica (which is the replica of highest energy) becomes:
 
 Fi = -Grad(V) + 2 (Grad(V) dot That) That :pre
 
-
-By default, the force acting on the first and last replicas is not altered so
-that during the NEB relaxation, these ending replicas relax toward local
-minima. However it is possible to use the key word {freeend} to allow either the
-initial or the final replica to relax toward a MEP while constraining its
-energy.  The interatomic force Fi for the free end image becomes :
-
-Fi = -Grad(V)+ (Grad(V) dot That + E-ETarget) That when Grad(V) dot That < 0 Fi
-= -Grad(V)+ (Grad(V) dot That + ETarget- E) That when Grad(V) dot That > 0
-
-where E is the energy of the free end replica and ETarget is the target energy.
-
-When the value {ini} ({final}) is used after the keyword {freeend}, the first
-(last) replica is considered as a free end. The target energy is set to the
-energy of the replica at starting of the NEB calculation. When the value
-{finaleini} or {final2eini} is used the last image is considered as a free end
-and the target energy is equal to the energy of the first replica (which can
-evolve during the NEB relaxation).  With the value {finaleini}, when the initial
-path is too far from the MEP, an intermediate repilica might relax "faster" and
-get a lower energy than the last replica. The benefit of the free end is then
-lost since this intermediate replica will relax toward a local minima. This
-behavior can be prevented by using the value {final2eini} which remove entirely
-the contribution of the gradient for all intermediate replica which have a lower
-energy than the initial one thus preventing these replicae to over-relax.  After
-converging a NEB with the {final2eini} value it is recommended to check that all
-intermediate replica have a larger energy than the initial replica. Finally note
-that if the last replica converges toward a local minimum with a larger energy
-than the energy of the first replica, a free end neb calculation with the value
-{finaleini} or {final2eini} cannot reach the convergence criteria.
+By default, the force acting on the first and last replicas is not
+altered so that during the NEB relaxation, these ending replicas relax
+toward local minima. However it is possible to use the key word
+{freeend} to allow either the initial or the final replica to relax
+toward a MEP while constraining its energy.  The interatomic force Fi
+for the free end image becomes :
+
+Fi = -Grad(V)+ (Grad(V) dot That + E-ETarget) That,  {when} Grad(V) dot That < 0
+Fi = -Grad(V)+ (Grad(V) dot That + ETarget- E) That, {when} Grad(V) dot That > 0
+:pre
+
+where E is the energy of the free end replica and ETarget is the
+target energy.
+
+When the value {ini} ({final}) is used after the keyword {freeend},
+the first (last) replica is considered as a free end. The target
+energy is set to the energy of the replica at starting of the NEB
+calculation. When the value {finaleini} or {final2eini} is used the
+last image is considered as a free end and the target energy is equal
+to the energy of the first replica (which can evolve during the NEB
+relaxation).  With the value {finaleini}, when the initial path is too
+far from the MEP, an intermediate repilica might relax "faster" and
+get a lower energy than the last replica. The benefit of the free end
+is then lost since this intermediate replica will relax toward a local
+minima. This behavior can be prevented by using the value {final2eini}
+which remove entirely the contribution of the gradient for all
+intermediate replica which have a lower energy than the initial one
+thus preventing these replicae to over-relax.  After converging a NEB
+with the {final2eini} value it is recommended to check that all
+intermediate replica have a larger energy than the initial
+replica. Finally note that if the last replica converges toward a
+local minimum with a larger energy than the energy of the first
+replica, a free end neb calculation with the value {finaleini} or
+{final2eini} cannot reach the convergence criteria.
 
 :line
 
-
-The keywords {idealpos} and {neigh} allow to specify how to parallel spring
-force is computed.  If the keyword {idealpos} is used or by default, the spring
-force is computed as suggested in "(E)"_#E :
+The keywords {idealpos} and {neigh} allow to specify how to parallel
+spring force is computed.  If the keyword {idealpos} is used or by
+default, the spring force is computed as suggested in "(E)"_#E :
    
-Fspringparallel=-{Kspring}* (RD-RDideal)/(2 meanDist)
+Fspringparallel=-{Kspring}* (RD-RDideal)/(2 meanDist) :pre
 
-where RD is the "reaction coordinate" see "neb"_neb.html section, and RDideal is
-the ideal RD for which all the images are equally spaced (i.e. RDideal =
-(i-1)*meanDist when the climbing image is off, where i is the replica
-number). The meanDist is the average distance between replicas.
+where RD is the "reaction coordinate" see "neb"_neb.html section, and
+RDideal is the ideal RD for which all the images are equally spaced
+(i.e. RDideal = (i-1)*meanDist when the climbing image is off, where i
+is the replica number). The meanDist is the average distance between
+replicas.
 
-If the keyword {neigh} is used, the parallel spring force is computed as in
-"(Henkelman1)"_#Henkelman1 by connecting each intermediate replica with the
-previous and the next image:
+If the keyword {neigh} is used, the parallel spring force is computed
+as in "(Henkelman1)"_#Henkelman1 by connecting each intermediate
+replica with the previous and the next image:
 
-Fspringparallel= {Kspring}* (|Ri+1 - Ri| - |Ri - Ri-1|)
+Fspringparallel= {Kspring}* (|Ri+1 - Ri| - |Ri - Ri-1|) :pre
 
-The parallel spring force associated with the key word idealpos should usually
-be more efficient at keeping the images equally spaced.
+The parallel spring force associated with the key word idealpos should
+usually be more efficient at keeping the images equally spaced.
 
 :line
 
-The keyword {perp} allows to add a spring force perpendicular to the path in
-order to prevent the path from becoming too kinky. It can improve significantly
-the convergence of the NEB when the resolution is poor (i.e. when too few images
-are used) (see "(Maras)"_#Maras).  The perpendicular spring force is given by
+The keyword {perp} allows to add a spring force perpendicular to the
+path in order to prevent the path from becoming too kinky. It can
+improve significantly the convergence of the NEB when the resolution
+is poor (i.e. when too few images are used) (see "(Maras)"_#Maras1).
+The perpendicular spring force is given by
 
-Fspringperp = {Kspringperp} * f(Ri-1,Ri,Ri+1) (Ri+1 + Ri-1 - 2 Ri)
+Fspringperp = {Kspringperp} * f(Ri-1,Ri,Ri+1) (Ri+1 + Ri-1 - 2 Ri) :pre
 
- f(Ri-1 Ri R+1) is a smooth scalar function of the angle Ri-1 Ri Ri+1. It is
- equal to 0 when the path is straight and is equal to 1 when the angle Ri-1 Ri
- Ri+1 is accute. f(Ri-1 Ri R+1) is defined in "(Jonsson)"_#Jonsson
+f(Ri-1 Ri R+1) is a smooth scalar function of the angle Ri-1 Ri
+Ri+1. It is equal to 0 when the path is straight and is equal to 1
+when the angle Ri-1 Ri Ri+1 is accute. f(Ri-1 Ri R+1) is defined in
+"(Jonsson)"_#Jonsson
 
 :line
 
 [Restart, fix_modify, output, run start/stop, minimize info:]
 
-No information about this fix is written to "binary restart files"_restart.html.
-None of the "fix_modify"_fix_modify.html options 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#howto_15.  No parameter of this fix can be
-used with the {start/stop} keywords of the "run"_run.html command.
+No information about this fix is written to "binary restart
+files"_restart.html.  None of the "fix_modify"_fix_modify.html options
+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#howto_15.  No parameter of this fix can
+be used with the {start/stop} keywords of the "run"_run.html command.
 
-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.
+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:]
 
-This command can only be used if LAMMPS was built with the REPLICA package.  See
-the "Making LAMMPS"_Section_start.html#start_3 section for more info on
-packages.
+This command can only be used if LAMMPS was built with the REPLICA
+package.  See the "Making LAMMPS"_Section_start.html#start_3 section
+for more info on packages.
 
 [Related commands:]
 
 "neb"_neb.html
 
-[Default:] none
+[Default:]
+
+none
 
-:link(Henkelman1) [(Henkelman1)] Henkelman and Jonsson, J Chem Phys, 113,
-9978-9985 (2000).
+:link(Henkelman1)
+[(Henkelman1)] Henkelman and Jonsson, J Chem Phys, 113, 9978-9985 (2000).
 
-:link(Henkelman2) [(Henkelman2)] Henkelman, Uberuaga, Jonsson, J Chem Phys, 113,
+:link(Henkelman2)
+[(Henkelman2)] Henkelman, Uberuaga, Jonsson, J Chem Phys, 113,
 9901-9904 (2000).
 
-:link(E) [(E)] E, Ren, Vanden-Eijnden, Phys Rev B, 66, 052301 (2002)
+:link(E)
+[(E)] E, Ren, Vanden-Eijnden, Phys Rev B, 66, 052301 (2002)
 
-:link(Jonsson) [(Jonsson)] Jonsson, Mills and Jacobsen, in Classical and Quantum
+:link(Jonsson)
+[(Jonsson)] Jonsson, Mills and Jacobsen, in Classical and Quantum
 Dynamics in Condensed Phase Simulations, edited by Berne, Ciccotti, and Coker
-Í‘World Scientific, Singapore, 1998Í’, p. 385
+World Scientific, Singapore, 1998, p. 385
 
-:link(Maras) [(Maras)] Maras, Trushin, Stukowski, Ala-Nissila, Jonsson, Comp
-Phys Comm, 205, 13-21 (2016)
+:link(Maras1)
+[(Maras)] Maras, Trushin, Stukowski, Ala-Nissila, Jonsson,
+Comp Phys Comm, 205, 13-21 (2016)
diff --git a/doc/src/neb.txt b/doc/src/neb.txt
index 966d1574a4..294bbdeb09 100644
--- a/doc/src/neb.txt
+++ b/doc/src/neb.txt
@@ -2,6 +2,7 @@
 
 :link(lws,http://lammps.sandia.gov)
 :link(ld,Manual.html)
+:link(lc,Section_commands.html#comm)
 
 :line
 
@@ -11,362 +12,416 @@ neb command :h3
 
 neb etol ftol N1 N2 Nevery file-style arg keyword :pre
 
-etol = stopping tolerance for energy (energy units) :ulb,l ftol = stopping
-tolerance for force (force units) :l N1 = max # of iterations (timesteps) to run
-initial NEB :l N2 = max # of iterations (timesteps) to run barrier-climbing NEB
-:l Nevery = print replica energies and reaction coordinates every this many
-timesteps :l file-style= {final} or {each} or {none} :l {final} arg = filename
-filename = file with initial coords for final replica coords for intermediate
-replicas are linearly interpolated between first and last replica {each} arg =
-filename filename = unique filename for each replica (except first) with its
-initial coords {none} arg = no argument all replicas assumed to already have
-their initial coords :pre keyword = {verbose} :pre :ule
+etol = stopping tolerance for energy (energy units) :ulb,l
+ftol = stopping tolerance for force (force units) :l
+N1 = max # of iterations (timesteps) to run initial NEB :l
+N2 = max # of iterations (timesteps) to run barrier-climbing NEB :l
+Nevery = print replica energies and reaction coordinates every this many timesteps :l
+file-style = {final} or {each} or {none} :l
+  {final} arg = filename
+    filename = file with initial coords for final replica
+      coords for intermediate replicas are linearly interpolated
+      between first and last replica
+  {each} arg = filename
+    filename = unique filename for each replica (except first)
+      with its initial coords
+  {none} arg = no argument all replicas assumed to already have
+      their initial coords :pre
+keyword = {verbose}
+:ule
 
 [Examples:]
 
-neb 0.1 0.0 1000 500 50 final coords.final neb 0.0 0.001 1000 500 50 each
-coords.initial.$i neb 0.0 0.001 1000 500 50 none verbose :pre
+neb 0.1 0.0 1000 500 50 final coords.final
+neb 0.0 0.001 1000 500 50 each coords.initial.$i
+neb 0.0 0.001 1000 500 50 none verbose :pre
 
 [Description:]
 
-Perform a nudged elastic band (NEB) calculation using multiple replicas of a
-system.  Two or more replicas must be used; the first and last are the end
-points of the transition path.
+Perform a nudged elastic band (NEB) calculation using multiple
+replicas of a system.  Two or more replicas must be used; the first
+and last are the end points of the transition path.
 
-NEB is a method for finding both the atomic configurations and height of the
-energy barrier associated with a transition state, e.g. for an atom to perform a
-diffusive hop from one energy basin to another in a coordinated fashion with its
-neighbors.  The implementation in LAMMPS follows the discussion in these 4
-papers: "(HenkelmanA)"_#HenkelmanA, "(HenkelmanB)"_#HenkelmanB,
-"(Nakano)"_#Nakano3 and "(Maras)"_#Maras.
+NEB is a method for finding both the atomic configurations and height
+of the energy barrier associated with a transition state, e.g. for an
+atom to perform a diffusive hop from one energy basin to another in a
+coordinated fashion with its neighbors.  The implementation in LAMMPS
+follows the discussion in these 4 papers: "(HenkelmanA)"_#HenkelmanA,
+"(HenkelmanB)"_#HenkelmanB, "(Nakano)"_#Nakano3 and "(Maras)"_#Maras2.
 
 Each replica runs on a partition of one or more processors.  Processor
-partitions are defined at run-time using the -partition command-line switch; see
-"Section 2.7"_Section_start.html#start_7 of the manual.  Note that if you have
-MPI installed, you can run a multi-replica simulation with more replicas
-(partitions) than you have physical processors, e.g you can run a 10-replica
-simulation on just one or two processors.  You will simply not get the
-performance speed-up you would see with one or more physical processors per
-replica.  See "Section 6.5"_Section_howto.html#howto_5 of the manual for further
+partitions are defined at run-time using the -partition command-line
+switch; see "Section 2.7"_Section_start.html#start_7 of the manual.
+Note that if you have MPI installed, you can run a multi-replica
+simulation with more replicas (partitions) than you have physical
+processors, e.g you can run a 10-replica simulation on just one or two
+processors.  You will simply not get the performance speed-up you
+would see with one or more physical processors per replica.  See
+"Section 6.5"_Section_howto.html#howto_5 of the manual for further
 discussion.
 
 NOTE: As explained below, a NEB calculation perfoms a damped dynamics
-minimization across all the replicas.  The mimimizer uses whatever timestep you
-have defined in your input script, via the "timestep"_timestep.html command.
-Often NEB will converge more quickly if you use a timestep about 10x larger than
-you would normally use for dynamics simulations.
-
-When a NEB calculation is performed, it is assumed that each replica is running
-the same system, though LAMMPS does not check for this.  I.e. the simulation
-domain, the number of atoms, the interaction potentials, and the starting
-configuration when the neb command is issued should be the same for every
-replica.
+minimization across all the replicas.  The mimimizer uses whatever
+timestep you have defined in your input script, via the
+"timestep"_timestep.html command.  Often NEB will converge more
+quickly if you use a timestep about 10x larger than you would normally
+use for dynamics simulations.
+
+When a NEB calculation is performed, it is assumed that each replica
+is running the same system, though LAMMPS does not check for this.
+I.e. the simulation domain, the number of atoms, the interaction
+potentials, and the starting configuration when the neb command is
+issued should be the same for every replica.
 
 In a NEB calculation each replica is connected to other replicas by
 inter-replica nudging forces.  These forces are imposed by the "fix
-neb"_fix_neb.html command, which must be used in conjunction with the neb
-command.  The group used to define the fix neb command defines the NEB atoms
-which are the only ones that inter-replica springs are applied to.  If the group
-does not include all atoms, then non-NEB atoms have no inter-replica springs and
-the forces they feel and their motion is computed in the usual way due only to
-other atoms within their replica.  Conceptually, the non-NEB atoms provide a
-background force field for the NEB atoms.  They can be allowed to move during
-the NEB minimization procedure (which will typically induce different
-coordinates for non-NEB atoms in different replicas), or held fixed using other
-LAMMPS commands such as "fix setforce"_fix_setforce.html.  Note that the
-"partition"_partition.html command can be used to invoke a command on a subset
-of the replicas, e.g. if you wish to hold NEB or non-NEB atoms fixed in only the
-end-point replicas.
-
-The initial atomic configuration for each of the replicas can be specified in
-different manners via the {file-style} setting, as discussed below.  Only atoms
-whose initial coordinates should differ from the current configuration need be
-specified.
-
-Conceptually, the initial and final configurations for the first replica should
-be states on either side of an energy barrier.
-
-As explained below, the initial configurations of intermediate replicas can be
-atomic coordinates interpolated in a linear fashion between the first and last
-replicas.  This is often adequate for simple transitions.  For more complex
-transitions, it may lead to slow convergence or even bad results if the minimum
-energy path (MEP, see below) of states over the barrier cannot be correctly
-converged to from such an initial path.  In this case, you will want to generate
-initial states for the intermediate replicas that are geometrically closer to
-the MEP and read them in.
+neb"_fix_neb.html command, which must be used in conjunction with the
+neb command.  The group used to define the fix neb command defines the
+NEB atoms which are the only ones that inter-replica springs are
+applied to.  If the group does not include all atoms, then non-NEB
+atoms have no inter-replica springs and the forces they feel and their
+motion is computed in the usual way due only to other atoms within
+their replica.  Conceptually, the non-NEB atoms provide a background
+force field for the NEB atoms.  They can be allowed to move during the
+NEB minimization procedure (which will typically induce different
+coordinates for non-NEB atoms in different replicas), or held fixed
+using other LAMMPS commands such as "fix setforce"_fix_setforce.html.
+Note that the "partition"_partition.html command can be used to invoke
+a command on a subset of the replicas, e.g. if you wish to hold NEB or
+non-NEB atoms fixed in only the end-point replicas.
+
+The initial atomic configuration for each of the replicas can be
+specified in different manners via the {file-style} setting, as
+discussed below.  Only atoms whose initial coordinates should differ
+from the current configuration need be specified.
+
+Conceptually, the initial and final configurations for the first
+replica should be states on either side of an energy barrier.
+
+As explained below, the initial configurations of intermediate
+replicas can be atomic coordinates interpolated in a linear fashion
+between the first and last replicas.  This is often adequate for
+simple transitions.  For more complex transitions, it may lead to slow
+convergence or even bad results if the minimum energy path (MEP, see
+below) of states over the barrier cannot be correctly converged to
+from such an initial path.  In this case, you will want to generate
+initial states for the intermediate replicas that are geometrically
+closer to the MEP and read them in.
 
 :line
 
-For a {file-style} setting of {final}, a filename is specified which contains
-atomic coordinates for zero or more atoms, in the format described below.  For
-each atom that appears in the file, the new coordinates are assigned to that
-atom in the final replica.  Each intermediate replica also assigns a new
-position to that atom in an interpolated manner.  This is done by using the
-current position of the atom as the starting point and the read-in position as
-the final point.  The distance between them is calculated, and the new position
-is assigned to be a fraction of the distance.  E.g. if there are 10 replicas,
-the 2nd replica will assign a position that is 10% of the distance along a line
-between the starting and final point, and the 9th replica will assign a position
-that is 90% of the distance along the line.  Note that for this procedure to
-produce consistent coordinates across all the replicas, the current coordinates
-need to be the same in all replicas.  LAMMPS does not check for this, but
-invalid initial configurations will likely result if it is not the case.
-
-NOTE: The "distance" between the starting and final point is calculated in a
-minimum-image sense for a periodic simulation box.  This means that if the two
-positions are on opposite sides of a box (periodic in that dimension), the
-distance between them will be small, because the periodic image of one of the
-atoms is close to the other.  Similarly, even if the assigned position resulting
-from the interpolation is outside the periodic box, the atom will be wrapped
+For a {file-style} setting of {final}, a filename is specified which
+contains atomic coordinates for zero or more atoms, in the format
+described below.  For each atom that appears in the file, the new
+coordinates are assigned to that atom in the final replica.  Each
+intermediate replica also assigns a new position to that atom in an
+interpolated manner.  This is done by using the current position of
+the atom as the starting point and the read-in position as the final
+point.  The distance between them is calculated, and the new position
+is assigned to be a fraction of the distance.  E.g. if there are 10
+replicas, the 2nd replica will assign a position that is 10% of the
+distance along a line between the starting and final point, and the
+9th replica will assign a position that is 90% of the distance along
+the line.  Note that for this procedure to produce consistent
+coordinates across all the replicas, the current coordinates need to
+be the same in all replicas.  LAMMPS does not check for this, but
+invalid initial configurations will likely result if it is not the
+case.
+
+NOTE: The "distance" between the starting and final point is
+calculated in a minimum-image sense for a periodic simulation box.
+This means that if the two positions are on opposite sides of a box
+(periodic in that dimension), the distance between them will be small,
+because the periodic image of one of the atoms is close to the other.
+Similarly, even if the assigned position resulting from the
+interpolation is outside the periodic box, the atom will be wrapped
 back into the box when the NEB calculation begins.
 
-For a {file-style} setting of {each}, a filename is specified which is assumed
-to be unique to each replica.  This can be done by using a variable in the
-filename, e.g.
-
-variable i equal part neb 0.0 0.001 1000 500 50 each coords.initial.$i :pre
-
-which in this case will substitute the partition ID (0 to N-1) for the variable
-I, which is also effectively the replica ID.  See the "variable"_variable.html
-command for other options, such as using world-, universe-, or uloop-style
-variables.
-
-Each replica (except the first replica) will read its file, formatted as
-described below, and for any atom that appears in the file, assign the specified
-coordinates to this atom.  The various files do not need to contain the same set
-of atoms.
-
-For a {file-style} setting of {none}, no filename is specified.  Each replica is
-assumed to already be in its initial configuration at the time the neb command
-is issued.  This allows each replica to define its own configuration by reading
-a replica-specific data or restart or dump file, via the
-"read_data"_read_data.html, "read_restart"_read_restart.html, or
-"read_dump"_read_dump.html commands.  The replica-specific names of these files
-can be specified as in the discussion above for the {each} file-style.  Also see
-the section below for how a NEB calculation can produce restart files, so that a
-long calculation can be restarted if needed.
-
-NOTE: None of the {file-style} settings change the initial configuration of any
-atom in the first replica.  The first replica must thus be in the correct
-initial configuration at the time the neb command is issued.
+For a {file-style} setting of {each}, a filename is specified which is
+assumed to be unique to each replica.  This can be done by using a
+variable in the filename, e.g.
+
+variable i equal part
+neb 0.0 0.001 1000 500 50 each coords.initial.$i :pre
+
+which in this case will substitute the partition ID (0 to N-1) for the
+variable I, which is also effectively the replica ID.  See the
+"variable"_variable.html command for other options, such as using
+world-, universe-, or uloop-style variables.
+
+Each replica (except the first replica) will read its file, formatted
+as described below, and for any atom that appears in the file, assign
+the specified coordinates to this atom.  The various files do not need
+to contain the same set of atoms.
+
+For a {file-style} setting of {none}, no filename is specified.  Each
+replica is assumed to already be in its initial configuration at the
+time the neb command is issued.  This allows each replica to define
+its own configuration by reading a replica-specific data or restart or
+dump file, via the "read_data"_read_data.html,
+"read_restart"_read_restart.html, or "read_dump"_read_dump.html
+commands.  The replica-specific names of these files can be specified
+as in the discussion above for the {each} file-style.  Also see the
+section below for how a NEB calculation can produce restart files, so
+that a long calculation can be restarted if needed.
+
+NOTE: None of the {file-style} settings change the initial
+configuration of any atom in the first replica.  The first replica
+must thus be in the correct initial configuration at the time the neb
+command is issued.
 
 :line
 
-A NEB calculation proceeds in two stages, each of which is a minimization
-procedure, performed via damped dynamics.  To enable this, you must first define
-a damped dynamics "min_style"_min_style.html, such as {quickmin} or {fire}.  The
-{cg}, {sd}, and {hftn} styles cannot be used, since they perform iterative line
-searches in their inner loop, which cannot be easily synchronized across
-multiple replicas.
-
-The minimizer tolerances for energy and force are set by {etol} and {ftol}, the
-same as for the "minimize"_minimize.html command.
-
-A non-zero {etol} means that the NEB calculation will terminate if the energy
-criterion is met by every replica.  The energies being compared to {etol} do not
-include any contribution from the inter-replica nudging forces, since these are
-non-conservative.  A non-zero {ftol} means that the NEB calculation will
-terminate if the force criterion is met by every replica.  The forces being
-compared to {ftol} include the inter-replica nudging forces.
-
-The maximum number of iterations in each stage is set by {N1} and {N2}.  These
-are effectively timestep counts since each iteration of damped dynamics is like
-a single timestep in a dynamics "run"_run.html.  During both stages, the
-potential energy of each replica and its normalized distance along the reaction
-path (reaction coordinate RD) will be printed to the screen and log file every
-{Nevery} timesteps.  The RD is 0 and 1 for the first and last replica.  For
-intermediate replicas, it is the cumulative distance (normalized by the total
-cumulative distance) between adjacent replicas, where "distance" is defined as
-the length of the 3N-vector of differences in atomic coordinates, where N is the
-number of NEB atoms involved in the transition.  These outputs allow you to
-monitor NEB's progress in finding a good energy barrier.  {N1} and {N2} must
-both be multiples of {Nevery}.
-
-In the first stage of NEB, the set of replicas should converge toward a minimum
-energy path (MEP) of conformational states that transition over a barrier.  The
-MEP for a transition is defined as a sequence of 3N-dimensional states, each of
-which has a potential energy gradient parallel to the MEP itself.  The
-configuration of highest energy along a MEP corresponds to a saddle point.  The
-replica states will also be roughly equally spaced along the MEP due to the
-inter-replica nugding force added by the "fix neb"_fix_neb.html command.
-
-In the second stage of NEB, the replica with the highest energy is selected and
-the inter-replica forces on it are converted to a force that drives its atom
-coordinates to the top or saddle point of the barrier, via the barrier-climbing
-calculation described in "(HenkelmanB)"_#HenkelmanB.  As before, the other
-replicas rearrange themselves along the MEP so as to be roughly equally spaced.
-
-When both stages are complete, if the NEB calculation was successful, the
-configurations of the replicas should be along (close to) the MEP and the
-replica with the highest energy should be an atomic configuration at (close to)
-the saddle point of the transition. The potential energies for the set of
-replicas represents the energy profile of the transition along the MEP.
+A NEB calculation proceeds in two stages, each of which is a
+minimization procedure, performed via damped dynamics.  To enable
+this, you must first define a damped dynamics
+"min_style"_min_style.html, such as {quickmin} or {fire}.  The {cg},
+{sd}, and {hftn} styles cannot be used, since they perform iterative
+line searches in their inner loop, which cannot be easily synchronized
+across multiple replicas.
+
+The minimizer tolerances for energy and force are set by {etol} and
+{ftol}, the same as for the "minimize"_minimize.html command.
+
+A non-zero {etol} means that the NEB calculation will terminate if the
+energy criterion is met by every replica.  The energies being compared
+to {etol} do not include any contribution from the inter-replica
+nudging forces, since these are non-conservative.  A non-zero {ftol}
+means that the NEB calculation will terminate if the force criterion
+is met by every replica.  The forces being compared to {ftol} include
+the inter-replica nudging forces.
+
+The maximum number of iterations in each stage is set by {N1} and
+{N2}.  These are effectively timestep counts since each iteration of
+damped dynamics is like a single timestep in a dynamics
+"run"_run.html.  During both stages, the potential energy of each
+replica and its normalized distance along the reaction path (reaction
+coordinate RD) will be printed to the screen and log file every
+{Nevery} timesteps.  The RD is 0 and 1 for the first and last replica.
+For intermediate replicas, it is the cumulative distance (normalized
+by the total cumulative distance) between adjacent replicas, where
+"distance" is defined as the length of the 3N-vector of differences in
+atomic coordinates, where N is the number of NEB atoms involved in the
+transition.  These outputs allow you to monitor NEB's progress in
+finding a good energy barrier.  {N1} and {N2} must both be multiples
+of {Nevery}.
+
+In the first stage of NEB, the set of replicas should converge toward
+a minimum energy path (MEP) of conformational states that transition
+over a barrier.  The MEP for a transition is defined as a sequence of
+3N-dimensional states, each of which has a potential energy gradient
+parallel to the MEP itself.  The configuration of highest energy along
+a MEP corresponds to a saddle point.  The replica states will also be
+roughly equally spaced along the MEP due to the inter-replica nugding
+force added by the "fix neb"_fix_neb.html command.
+
+In the second stage of NEB, the replica with the highest energy is
+selected and the inter-replica forces on it are converted to a force
+that drives its atom coordinates to the top or saddle point of the
+barrier, via the barrier-climbing calculation described in
+"(HenkelmanB)"_#HenkelmanB.  As before, the other replicas rearrange
+themselves along the MEP so as to be roughly equally spaced.
+
+When both stages are complete, if the NEB calculation was successful,
+the configurations of the replicas should be along (close to) the MEP
+and the replica with the highest energy should be an atomic
+configuration at (close to) the saddle point of the transition. The
+potential energies for the set of replicas represents the energy
+profile of the transition along the MEP.
 
 :line
 
-A few other settings in your input script are required or advised to perform a
-NEB calculation.  See the NOTE about the choice of timestep at the beginning of
-this doc page.
+A few other settings in your input script are required or advised to
+perform a NEB calculation.  See the NOTE about the choice of timestep
+at the beginning of this doc page.
 
 An atom map must be defined which it is not by default for "atom_style
-atomic"_atom_style.html problems.  The "atom_modify map"_atom_modify.html
-command can be used to do this.
-
-The minimizers in LAMMPS operate on all atoms in your system, even non-NEB
-atoms, as defined above.  To prevent non-NEB atoms from moving during the
-minimization, you should use the "fix setforce"_fix_setforce.html command to set
-the force on each of those atoms to 0.0.  This is not required, and may not even
-be desired in some cases, but if those atoms move too far (e.g. because the
-initial state of your system was not well-minimized), it can cause problems for
-the NEB procedure.
-
-The damped dynamics "minimizers"_min_style.html, such as {quickmin} and {fire}),
-adjust the position and velocity of the atoms via an Euler integration step.
-Thus you must define an appropriate "timestep"_timestep.html to use with NEB.
-As mentioned above, NEB will often converge more quickly if you use a timestep
-about 10x larger than you would normally use for dynamics simulations.
+atomic"_atom_style.html problems.  The "atom_modify
+map"_atom_modify.html command can be used to do this.
+
+The minimizers in LAMMPS operate on all atoms in your system, even
+non-NEB atoms, as defined above.  To prevent non-NEB atoms from moving
+during the minimization, you should use the "fix
+setforce"_fix_setforce.html command to set the force on each of those
+atoms to 0.0.  This is not required, and may not even be desired in
+some cases, but if those atoms move too far (e.g. because the initial
+state of your system was not well-minimized), it can cause problems
+for the NEB procedure.
+
+The damped dynamics "minimizers"_min_style.html, such as {quickmin}
+and {fire}), adjust the position and velocity of the atoms via an
+Euler integration step.  Thus you must define an appropriate
+"timestep"_timestep.html to use with NEB.  As mentioned above, NEB
+will often converge more quickly if you use a timestep about 10x
+larger than you would normally use for dynamics simulations.
 
 :line
 
-Each file read by the neb command containing atomic coordinates used to
-initialize one or more replicas must be formatted as follows.
+Each file read by the neb command containing atomic coordinates used
+to initialize one or more replicas must be formatted as follows.
 
-The file can be ASCII text or a gzipped text file (detected by a .gz suffix).
-The file can contain initial blank lines or comment lines starting with "#"
-which are ignored.  The first non-blank, non-comment line should list N = the
-number of lines to follow.  The N successive lines contain the following
-information:
+The file can be ASCII text or a gzipped text file (detected by a .gz
+suffix).  The file can contain initial blank lines or comment lines
+starting with "#" which are ignored.  The first non-blank, non-comment
+line should list N = the number of lines to follow.  The N successive
+lines contain the following information:
 
-ID1 x1 y1 z1 ID2 x2 y2 z2 ...  IDN xN yN zN :pre
+ID1 x1 y1 z1
+ID2 x2 y2 z2
+...
+IDN xN yN zN :pre
 
-The fields are the atom ID, followed by the x,y,z coordinates.  The lines can be
-listed in any order.  Additional trailing information on the line is OK, such as
-a comment.
+The fields are the atom ID, followed by the x,y,z coordinates.  The
+lines can be listed in any order.  Additional trailing information on
+the line is OK, such as a comment.
 
-Note that for a typical NEB calculation you do not need to specify initial
-coordinates for very many atoms to produce differing starting and final replicas
-whose intermediate replicas will converge to the energy barrier.  Typically only
-new coordinates for atoms geometrically near the barrier need be specified.
+Note that for a typical NEB calculation you do not need to specify
+initial coordinates for very many atoms to produce differing starting
+and final replicas whose intermediate replicas will converge to the
+energy barrier.  Typically only new coordinates for atoms
+geometrically near the barrier need be specified.
 
-Also note there is no requirement that the atoms in the file correspond to the
-NEB atoms in the group defined by the "fix neb"_fix_neb.html command.  Not every
-NEB atom need be in the file, and non-NEB atoms can be listed in the file.
+Also note there is no requirement that the atoms in the file
+correspond to the NEB atoms in the group defined by the "fix
+neb"_fix_neb.html command.  Not every NEB atom need be in the file,
+and non-NEB atoms can be listed in the file.
 
 :line
 
-Four kinds of output can be generated during a NEB calculation: energy barrier
-statistics, thermodynamic output by each replica, dump files, and restart files.
-
-When running with multiple partitions (each of which is a replica in this case),
-the print-out to the screen and master log.lammps file contains a line of
-output, printed once every {Nevery} timesteps.  It contains the timestep, the
-maximum force per replica, the maximum force per atom (in any replica),
-potential gradients in the initial, final, and climbing replicas, the forward
-and backward energy barriers, the total reaction coordinate (RDT), and the
-normalized reaction coordinate and potential energy of each replica.
-
-The "maximum force per replica" is the two-norm of the 3N-length force vector
-for the atoms in each replica, maximized across replicas, which is what the
-{ftol} setting is checking against.  In this case, N is all the atoms in each
-replica.  The "maximum force per atom" is the maximum force component of any
-atom in any replica.  The potential gradients are the two-norm of the 3N-length
-force vector solely due to the interaction potential i.e.  without adding in
-inter-replica forces.
-
-The "reaction coordinate" (RD) for each replica is the two-norm of the 3N-length
-vector of distances between its atoms and the preceding replica's atoms, added
-to the RD of the preceding replica. The RD of the first replica RD1 = 0.0; the
-RD of the final replica RDN = RDT, the total reaction coordinate.  The
-normalized RDs are divided by RDT, so that they form a monotonically increasing
-sequence from zero to one. When computing RD, N only includes the atoms being
-operated on by the fix neb command.
-
-The forward (reverse) energy barrier is the potential energy of the highest
-replica minus the energy of the first (last) replica.
-
-Supplementary informations for all replicas can be printed out to the screen and
-master log.lammps file by adding the verbose keyword. These informations include
-the following.  The "path angle" (pathangle) for the replica i which is the
-angle between the 3N-length vectors (Ri-1 - Ri) and (Ri+1 - Ri) (where Ri is the
-atomic coordinates of replica i). A "path angle" of 180 indicates that replicas
-i-1, i and i+1 are aligned.  "angletangrad" is the angle between the 3N-length
-tangent vector and the 3N-length force vector at image i. The tangent vector is
-calculated as in "(HenkelmanA)"_#HenkelmanA for all intermediate replicas and at
-R2 - R1 and RM - RM-1 for the first and last replica, respectively.  "anglegrad"
-is the angle between the 3N-length energy gradient vector of replica i and that
-of replica i+1. It is not defined for the final replica and reads nan.  gradV is
-the norm of the energy gradient of image i.  ReplicaForce is the two-norm of the
-3N-length force vector (including nudging forces) for replica i.  MaxAtomForce
-is the maximum force component of any atom in replica i.
+Four kinds of output can be generated during a NEB calculation: energy
+barrier statistics, thermodynamic output by each replica, dump files,
+and restart files.
+
+When running with multiple partitions (each of which is a replica in
+this case), the print-out to the screen and master log.lammps file
+contains a line of output, printed once every {Nevery} timesteps.  It
+contains the timestep, the maximum force per replica, the maximum
+force per atom (in any replica), potential gradients in the initial,
+final, and climbing replicas, the forward and backward energy
+barriers, the total reaction coordinate (RDT), and the normalized
+reaction coordinate and potential energy of each replica.
+
+The "maximum force per replica" is the two-norm of the 3N-length force
+vector for the atoms in each replica, maximized across replicas, which
+is what the {ftol} setting is checking against.  In this case, N is
+all the atoms in each replica.  The "maximum force per atom" is the
+maximum force component of any atom in any replica.  The potential
+gradients are the two-norm of the 3N-length force vector solely due to
+the interaction potential i.e.  without adding in inter-replica
+forces.
+
+The "reaction coordinate" (RD) for each replica is the two-norm of the
+3N-length vector of distances between its atoms and the preceding
+replica's atoms, added to the RD of the preceding replica. The RD of
+the first replica RD1 = 0.0; the RD of the final replica RDN = RDT,
+the total reaction coordinate.  The normalized RDs are divided by RDT,
+so that they form a monotonically increasing sequence from zero to
+one. When computing RD, N only includes the atoms being operated on by
+the fix neb command.
+
+The forward (reverse) energy barrier is the potential energy of the
+highest replica minus the energy of the first (last) replica.
+
+Supplementary informations for all replicas can be printed out to the
+screen and master log.lammps file by adding the verbose keyword. These
+informations include the following.  The "path angle" (pathangle) for
+the replica i which is the angle between the 3N-length vectors (Ri-1 -
+Ri) and (Ri+1 - Ri) (where Ri is the atomic coordinates of replica
+i). A "path angle" of 180 indicates that replicas i-1, i and i+1 are
+aligned.  "angletangrad" is the angle between the 3N-length tangent
+vector and the 3N-length force vector at image i. The tangent vector
+is calculated as in "(HenkelmanA)"_#HenkelmanA for all intermediate
+replicas and at R2 - R1 and RM - RM-1 for the first and last replica,
+respectively.  "anglegrad" is the angle between the 3N-length energy
+gradient vector of replica i and that of replica i+1. It is not
+defined for the final replica and reads nan.  gradV is the norm of the
+energy gradient of image i.  ReplicaForce is the two-norm of the
+3N-length force vector (including nudging forces) for replica i.
+MaxAtomForce is the maximum force component of any atom in replica i.
 
 When a NEB calculation does not converge properly, these suplementary
-informations can help understanding what is going wrong. For instance when the
-path angle becomes accute the definition of tangent used in the NEB calculation
-is questionable and the NEB cannot may diverge "(Maras)"_#Maras.
+informations can help understanding what is going wrong. For instance
+when the path angle becomes accute the definition of tangent used in
+the NEB calculation is questionable and the NEB cannot may diverge
+"(Maras)"_#Maras2.
  
 
-When running on multiple partitions, LAMMPS produces additional log files for
-each partition, e.g. log.lammps.0, log.lammps.1, etc.  For a NEB calculation,
-these contain the thermodynamic output for each replica.
-
-If "dump"_dump.html commands in the input script define a filename that includes
-a {universe} or {uloop} style "variable"_variable.html, then one dump file (per
-dump command) will be created for each replica.  At the end of the NEB
-calculation, the final snapshot in each file will contain the sequence of
-snapshots that transition the system over the energy barrier.  Earlier snapshots
-will show the convergence of the replicas to the MEP.
+When running on multiple partitions, LAMMPS produces additional log
+files for each partition, e.g. log.lammps.0, log.lammps.1, etc.  For a
+NEB calculation, these contain the thermodynamic output for each
+replica.
 
-Likewise, "restart"_restart.html filenames can be specified with a {universe} or
-{uloop} style "variable"_variable.html, to generate restart files for each
-replica.  These may be useful if the NEB calculation fails to converge properly
-to the MEP, and you wish to restart the calculation from an intermediate point
-with altered parameters.
+If "dump"_dump.html commands in the input script define a filename
+that includes a {universe} or {uloop} style "variable"_variable.html,
+then one dump file (per dump command) will be created for each
+replica.  At the end of the NEB calculation, the final snapshot in
+each file will contain the sequence of snapshots that transition the
+system over the energy barrier.  Earlier snapshots will show the
+convergence of the replicas to the MEP.
+
+Likewise, "restart"_restart.html filenames can be specified with a
+{universe} or {uloop} style "variable"_variable.html, to generate
+restart files for each replica.  These may be useful if the NEB
+calculation fails to converge properly to the MEP, and you wish to
+restart the calculation from an intermediate point with altered
+parameters.
 
 There are 2 Python scripts provided in the tools/python directory,
-neb_combine.py and neb_final.py, which are useful in analyzing output from a NEB
-calculation.  Assume a NEB simulation with M replicas, and the NEB atoms labeled
-with a specific atom type.
-
-The neb_combine.py script extracts atom coords for the NEB atoms from all M dump
-files and creates a single dump file where each snapshot contains the NEB atoms
-from all the replicas and one copy of non-NEB atoms from the first replica
-(presumed to be identical in other replicas).  This can be visualized/animated
-to see how the NEB atoms relax as the NEB calculation proceeds.
-
-The neb_final.py script extracts the final snapshot from each of the M dump
-files to create a single dump file with M snapshots.  This can be visualized to
-watch the system make its transition over the energy barrier.
+neb_combine.py and neb_final.py, which are useful in analyzing output
+from a NEB calculation.  Assume a NEB simulation with M replicas, and
+the NEB atoms labeled with a specific atom type.
+
+The neb_combine.py script extracts atom coords for the NEB atoms from
+all M dump files and creates a single dump file where each snapshot
+contains the NEB atoms from all the replicas and one copy of non-NEB
+atoms from the first replica (presumed to be identical in other
+replicas).  This can be visualized/animated to see how the NEB atoms
+relax as the NEB calculation proceeds.
+
+The neb_final.py script extracts the final snapshot from each of the M
+dump files to create a single dump file with M snapshots.  This can be
+visualized to watch the system make its transition over the energy
+barrier.
 
 To illustrate, here are images from the final snapshot produced by the
-neb_combine.py script run on the dump files produced by the two example input
-scripts in examples/neb.  Click on them to see a larger image.
+neb_combine.py script run on the dump files produced by the two
+example input scripts in examples/neb.  Click on them to see a larger
+image.
 
-:image(JPG/hop1_small.jpg,JPG/hop1.jpg) :image(JPG/hop2_small.jpg,JPG/hop2.jpg)
+:image(JPG/hop1_small.jpg,JPG/hop1.jpg)
+:image(JPG/hop2_small.jpg,JPG/hop2.jpg)
 
 :line
 
 [Restrictions:]
 
-This command can only be used if LAMMPS was built with the REPLICA package.  See
-the "Making LAMMPS"_Section_start.html#start_3 section for more info on
-packages.
+This command can only be used if LAMMPS was built with the REPLICA
+package.  See the "Making LAMMPS"_Section_start.html#start_3 section
+for more info on packages.
+
+:line
+
+[Related commands:]
 
-:line [Related commands:]
+"prd"_prd.html, "temper"_temper.html, "fix langevin"_fix_langevin.html,
+"fix viscous"_fix_viscous.html
 
-"prd"_prd.html, "temper"_temper.html, "fix langevin"_fix_langevin.html, "fix
-viscous"_fix_viscous.html
+[Default:]
 
-[Default:] none
+none
 
 :line
 
-:link(HenkelmanA) [(HenkelmanA)] Henkelman and Jonsson, J Chem Phys, 113,
-9978-9985 (2000).
+:link(HenkelmanA)
+[(HenkelmanA)] Henkelman and Jonsson, J Chem Phys, 113, 9978-9985 (2000).
 
-:link(HenkelmanB) [(HenkelmanB)] Henkelman, Uberuaga, Jonsson, J Chem Phys, 113,
+:link(HenkelmanB)
+[(HenkelmanB)] Henkelman, Uberuaga, Jonsson, J Chem Phys, 113,
 9901-9904 (2000).
 
-:link(Nakano3) [(Nakano)] Nakano, Comp Phys Comm, 178, 280-289 (2008).
+:link(Nakano3)
+[(Nakano)] Nakano, Comp Phys Comm, 178, 280-289 (2008).
 
-:link(Maras) [(Maras)] Maras, Trushin, Stukowski, Ala-Nissila, Jonsson, Comp
-Phys Comm, 205, 13-21 (2016)
+:link(Maras2)
+[(Maras)] Maras, Trushin, Stukowski, Ala-Nissila, Jonsson,
+Comp Phys Comm, 205, 13-21 (2016)
-- 
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