git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@4917 f3b2605a-c512-4ea7-a41b-209d697bcdaa

doc/min_style.html

@@ -55,15 +55,18 @@ some situations.
 <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.
+each atom.  The velocity of each atom is initialized to 0.0 by this
+style, at the beginning of a minimization.
 </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.
+the velocity non-parallel to the current force vector.  The velocity
+of each atom is initialized to 0.0 by this style, at the beginning of
+a minimization.
 </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.
+nudged elastic band (NEB) 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
@@ -90,7 +93,7 @@ Jonsson, Mills, Jacobsen.
 </P>
 <A NAME = "Bitzek"></A>
 
-<P><B><I>Bitzek</I></B> Bitzek, Koskinen, Gahler, Moseler, Gumbsch, Phys Rev Lett,
+<P><B>(Bitzek)</B> Bitzek, Koskinen, Gahler, Moseler, Gumbsch, Phys Rev Lett,
 97, 170201 (2006).
 </P>
 </HTML>

doc/min_style.txt

@@ -51,15 +51,18 @@ 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.
+each atom.  The velocity of each atom is initialized to 0.0 by this
+style, at the beginning of a minimization.
 
 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.
+the velocity non-parallel to the current force vector.  The velocity
+of each atom is initialized to 0.0 by this style, at the beginning of
+a minimization.
 
 Either the {quickmin} and {fire} styles are useful in the context of
-nudged elastic band (NEB} calculations via the "neb"_neb.html command.
+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
@@ -84,6 +87,6 @@ min_style cg :pre
 Jonsson, Mills, Jacobsen.
 
 :link(Bitzek)
-[{Bitzek}] Bitzek, Koskinen, Gahler, Moseler, Gumbsch, Phys Rev Lett,
+[(Bitzek)] Bitzek, Koskinen, Gahler, Moseler, Gumbsch, Phys Rev Lett,
 97, 170201 (2006).
 

doc/minimize.html

@@ -66,6 +66,12 @@ 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>IMPORTANT NOTE: <I>Etol</I> should be set to 0.0 when using the <I>quickmin</I>
+or <I>fire</I> <A HREF = "min_style.html">minimization styles</A>.  This is because they
+periodically reset velocities to 0.0 and take a zero-length step which
+will appear as a 0.0 energy change, stopping the minimizer if <I>etol</I>
+is finite.
+</P>
 <P>The objective function being minimized is the total potential energy
 of the system as a function of the N atom coordinates:
 </P>

doc/minimize.txt

@@ -63,6 +63,12 @@ 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.
 
+IMPORTANT NOTE: {Etol} should be set to 0.0 when using the {quickmin}
+or {fire} "minimization styles"_min_style.html.  This is because they
+periodically reset velocities to 0.0 and take a zero-length step which
+will appear as a 0.0 energy change, stopping the minimizer if {etol}
+is finite.
+
 The objective function being minimized is the total potential energy
 of the system as a function of the N atom coordinates:
 

doc/neb.html

@@ -30,8 +30,8 @@ neb 1.0e-6 0.001 1000 500 50 coords.final
 <P><B>Description:</B>
 </P>
 <P>Perform a nudged elastic band (NEB) calculation using multiple
-replicas of a system.  Three or more replicas must be used, two of
+replicas of a system.  Two or more replicas must be used, two of which
-which are the end points of the transition path.
+are the end points of the transition path.
 </P>
 <P>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
@@ -72,14 +72,13 @@ procedure, but they will not be part of the barrier finding procedure.
 <P>The "starting configuration" for NEB should be a state with the NEB
 atoms (and all other atoms) having coordinates on one side of the
 energy barrier.  These coordinates will be assigned to the first
-replica #1.  The coordinates should be close to a local energy minimum
+replica #1.  The coordinates should be close to a local energy
-and the velocities should be zeroed.  A perfect energy minimum is not
+minimum.  A perfect energy minimum is not required, since NEB runs via
-required (nor are zero velocities), since NEB runs via damped dynamics
+damped dynamics which will tend to drive the configuration of replica
-which will tend to drive the configuration of replica #1 to a true
+#1 to a true energy minimum, but you will typically get better
-energy minimum, but you will typically get better convergence if the
+convergence if the initial state is already at a minimum.  For
-initial state is already at a minimum.  For example, for a system with
+example, for a system with a free surface, the surface should be fully
-a free surface, the surface should be fully relaxed before attempting
+relaxed before attempting a NEB calculation.
-a NEB calculation.
 </P>
 <P>The final configuration is specified in the input <I>filename</I>, which is
 formatted as described below.  Only coordinates for NEB atoms or a
@@ -167,11 +166,6 @@ 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.
 </P>
-<P>Similarly, you should initialize the velocity of all NEB atoms (and
-non-NEB atoms if they are free to move) in your system to 0.0 before
-invoking the neb command.  This gives the minimizer a consistent zero
-velocity to start its damped dynamics with.
-</P>
 <P>The damped dynamics <A HREF = "min_style.html">minimizers</A>, such as <I>quickmin</I>
 and <I>fire</I>), adjust the position and velocity of the atoms via an
 Euler integration step.  Thus you must define an appropriate

doc/neb.txt

@@ -27,8 +27,8 @@ neb 1.0e-6 0.001 1000 500 50 coords.final :pre
 [Description:]
 
 Perform a nudged elastic band (NEB) calculation using multiple
-replicas of a system.  Three or more replicas must be used, two of
+replicas of a system.  Two or more replicas must be used, two of which
-which are the end points of the transition path.
+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
@@ -69,14 +69,13 @@ procedure, but they will not be part of the barrier finding procedure.
 The "starting configuration" for NEB should be a state with the NEB
 atoms (and all other atoms) having coordinates on one side of the
 energy barrier.  These coordinates will be assigned to the first
-replica #1.  The coordinates should be close to a local energy minimum
+replica #1.  The coordinates should be close to a local energy
-and the velocities should be zeroed.  A perfect energy minimum is not
+minimum.  A perfect energy minimum is not required, since NEB runs via
-required (nor are zero velocities), since NEB runs via damped dynamics
+damped dynamics which will tend to drive the configuration of replica
-which will tend to drive the configuration of replica #1 to a true
+#1 to a true energy minimum, but you will typically get better
-energy minimum, but you will typically get better convergence if the
+convergence if the initial state is already at a minimum.  For
-initial state is already at a minimum.  For example, for a system with
+example, for a system with a free surface, the surface should be fully
-a free surface, the surface should be fully relaxed before attempting
+relaxed before attempting a NEB calculation.
-a NEB calculation.
 
 The final configuration is specified in the input {filename}, which is
 formatted as described below.  Only coordinates for NEB atoms or a
@@ -164,11 +163,6 @@ 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.
 
-Similarly, you should initialize the velocity of all NEB atoms (and
-non-NEB atoms if they are free to move) in your system to 0.0 before
-invoking the neb command.  This gives the minimizer a consistent zero
-velocity to start its damped dynamics with.
-
 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