git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@11398 f3b2605a-c512-4ea7-a41b-209d697bcdaa

doc/min_style.html

@@ -68,6 +68,11 @@ a minimization.
 <P>Either the <I>quickmin</I> and <I>fire</I> styles are useful in the context of
 nudged elastic band (NEB) calculations via the <A HREF = "neb.html">neb</A> command.
 </P>
+<P>IMPORTANT NOTE: The damped dynamic minimizers use whatever timestep
+you have defined via the <A HREF = "timestep.html">timestep</A> command.  Often they
+will converge more quickly if you use a timestep about 10x larger than
+you would normally use for dynamics simulations.
+</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>

doc/min_style.txt

@@ -64,6 +64,11 @@ 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.
 
+IMPORTANT NOTE: The damped dynamic minimizers use whatever timestep
+you have defined via the "timestep"_timestep.html command.  Often they
+will converge more quickly if you use a timestep about 10x larger than
+you would normally use for dynamics simulations.
+
 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

doc/minimize.html

@@ -63,12 +63,18 @@ 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 = "timestep.html">timestep</A> be defined.
-<A HREF = "run.html">running dynamics</A> with the system, though it may be more
-efficient to use a larger timestep.
 </P>
-<P>The objective function being minimized is the total potential energy
+<P>IMPORTANT NOTE: The damped dynamic minimizers use whatever timestep
-of the system as a function of the N atom coordinates:
+you have defined via the <A HREF = "timestep.html">timestep</A> command.  Often they
+will converge more quickly if you use a timestep about 10x larger than
+you would normally use for dynamics simulations.
+</P>
+<HR>
+
+<P>In all cases, the objective function being minimized is the total
+potential energy of the system as a function of the N atom
+coordinates:
 </P>
 <CENTER><IMG SRC = "Eqs/min_energy.jpg">
 </CENTER>

doc/minimize.txt

@@ -60,12 +60,18 @@ 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
+"timestep"_timestep.html be defined.
-"running dynamics"_run.html with the system, though it may be more
-efficient to use a larger timestep.
 
-The objective function being minimized is the total potential energy
+IMPORTANT NOTE: The damped dynamic minimizers use whatever timestep
-of the system as a function of the N atom coordinates:
+you have defined via the "timestep"_timestep.html command.  Often they
+will converge more quickly if you use a timestep about 10x larger than
+you would normally use for dynamics simulations.
+
+:line
+
+In all cases, the objective function being minimized is the total
+potential energy of the system as a function of the N atom
+coordinates:
 
 :c,image(Eqs/min_energy.jpg)
 

doc/neb.html

@@ -70,12 +70,12 @@ for further discussion.
 <P>IMPORTANT NOTE: The current NEB implementation in LAMMPS only allows
 there to be one processor per replica.
 </P>
-<P>IMPORTANT NOTE: As explained below, a NEB calculation perfoms a
+<P>IMPORTANT NOTE: As explained below, a NEB calculation perfoms a damped
-damped-dynamics minimization across all the replicas.  This will use
+dynamics minimization across all the replicas.  The mimimizer uses
 whatever timestep you have defined in your input script, via the
-<A HREF = "timestep.html">timestep</A> command.  You may get faster convergence for
+<A HREF = "timestep.html">timestep</A> command.  Often NEB will converge more
-a NEB calculation if you use a larger timestep than you would normally
+quickly if you use a timestep about 10x larger than you would normally
-use for dynamics with the same system.
+use for dynamics simulations.
 </P>
 <P>When a NEB calculation is performed, it is assumed that each replica
 is running the same system, though LAMMPS does not check for this.

doc/neb.txt

@@ -60,12 +60,12 @@ for further discussion.
 IMPORTANT NOTE: The current NEB implementation in LAMMPS only allows
 there to be one processor per replica.
 
-IMPORTANT NOTE: As explained below, a NEB calculation perfoms a
+IMPORTANT NOTE: As explained below, a NEB calculation perfoms a damped
-damped-dynamics minimization across all the replicas.  This will use
+dynamics minimization across all the replicas.  The mimimizer uses
 whatever timestep you have defined in your input script, via the
-"timestep"_timestep.html command.  You may get faster convergence for
+"timestep"_timestep.html command.  Often NEB will converge more
-a NEB calculation if you use a larger timestep than you would normally
+quickly if you use a timestep about 10x larger than you would normally
-use for dynamics with the same system.
+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.

doc/tad.html

@@ -44,8 +44,9 @@
     N1 = max # of iterations (timesteps) to run initial NEB 
     N2 = max # of iterations (timesteps) to run barrier-climbing NEB
     Nevery = print NEB statistics every this many timesteps
-  <I>min_style</I> value = <I>cg</I> or <I>hftn</I> or <I>sd</I> or <I>quickmin</I> or <I>fire</I>
   <I>neb_style</I> value = <I>quickmin</I> or <I>fire</I>
+  <I>neb_step</I> value = dtneb
+    dtneb = timestep for NEB damped dynamics minimization
   <I>neb_log</I> value = file where NEB statistics are printed 
 </PRE>
 
@@ -132,9 +133,11 @@ check is performed by quenching the system and comparing the resulting
 atom coordinates to the coordinates from the previous basin.
 </P>
 <P>A quench is an energy minimization and is performed by whichever
-algorithm has been defined by the <I>min</I> and <I>min_style</I> keywords or
+algorithm has been defined by the <A HREF = "min_style.html">min_style</A> command;
-their default values. Note that typically, you do not need to perform
+its default is the CG minimizer.  The tolerances and limits for each
-a highly-converged minimization to detect a transition event.
+quench can be set by the <I>min</I> keyword.  Note that typically, you do
+not need to perform a highly-converged minimization to detect a
+transition event.
 </P>
 <P>The event check is performed by a compute with the specified
 <I>compute-ID</I>.  Currently there is only one compute that works with the
@@ -145,11 +148,17 @@ event/displace</A> checks whether any atom in
 the compute group has moved further than a specified threshold
 distance.  If so, an "event" has occurred.
 </P>
-<P>The neb calculation is similar to that invoked by the <A HREF = "neb.html">neb</A>
+<P>The NEB calculation is similar to that invoked by the <A HREF = "neb.html">neb</A>
 command, except that the final state is generated internally, instead
-of being read in from a file. The TAD implementation provides default
+of being read in from a file.  The style of minimization performed by
-values for the NEB settings, which can be overridden using the <I>neb</I>
+NEB is determined by the <I>neb_style</I> keyword and must be a damped
-and <I>neb_style</I> keywords.
+dynamics minimizer.  The tolerances and limits for each NEB
+calculation can be set by the <I>neb</I> keyword.  As discussed on the
+<A HREF = "neb.html">neb</A>, it is often advantageous to use a larger timestep for
+NEB than for normal dyanmics.  Since the size of the timestep set by
+the <A HREF = "timestep.html">timestep</A> command is used by TAD for performing
+dynamics, there is a <I>neb_step</I> keyword which can be used to set a
+larger timestep for each NEB calculation if desired.
 </P>
 <HR>
 
@@ -211,7 +220,7 @@ while the global event number, energy barrier, and
 in the immediately preceding block of detected events.  
 The low-temperature event time <I>t_lo</I> is incremented by <I>delt_lo</I>.
 </P>
-<P>The NEB statistics are written to the file specified by the <I>neb_log</I>
+<P>NEB statistics are written to the file specified by the <I>neb_log</I>
 keyword. If the keyword value is "none", then no NEB statistics are
 printed out. The statistics are written every <I>Nevery</I> timesteps.  See
 the <A HREF = "neb.html">neb</A> command for a full description of the NEB
@@ -301,8 +310,8 @@ dt/reset</A> and <A HREF = "fix_deposit.html">fix deposit</A>.
 <P><B>Default:</B> 
 </P>
 <P>The option defaults are <I>min</I> = 0.1 0.1 40 50, <I>neb</I> = 0.01 100 100
-10, <I>min_style</I> = <I>cg</I>, <I>neb_style</I> = <I>quickmin</I>, and <I>neb_log</I> =
+10, <I>neb_style</I> = <I>quickmin</I>, <I>neb_step</I> = the same timestep set by
-"none"
+the <A HREF = "timestep.html">timestep</A> command, and <I>neb_log</I> = "none".
 </P>
 <HR>
 

doc/tad.txt

@@ -33,8 +33,9 @@ keyword = {min} or {neb} or {min_style} or {neb_style} or {neb_log} :l
     N1 = max # of iterations (timesteps) to run initial NEB 
     N2 = max # of iterations (timesteps) to run barrier-climbing NEB
     Nevery = print NEB statistics every this many timesteps
-  {min_style} value = {cg} or {hftn} or {sd} or {quickmin} or {fire}
   {neb_style} value = {quickmin} or {fire}
+  {neb_step} value = dtneb
+    dtneb = timestep for NEB damped dynamics minimization
   {neb_log} value = file where NEB statistics are printed :pre
 
 :ule
@@ -95,7 +96,6 @@ partitions remain idle. See "Section_howto
 5"_Section_howto.html#howto_5 of the manual for further discussion of
 multi-replica simulations.
 
-
 A TAD run has several stages, which are repeated each time an event is
 performed.  The logic for a TAD run is as follows:
 
@@ -122,9 +122,11 @@ check is performed by quenching the system and comparing the resulting
 atom coordinates to the coordinates from the previous basin.
 
 A quench is an energy minimization and is performed by whichever
-algorithm has been defined by the {min} and {min_style} keywords or
+algorithm has been defined by the "min_style"_min_style.html command;
-their default values. Note that typically, you do not need to perform
+its default is the CG minimizer.  The tolerances and limits for each
-a highly-converged minimization to detect a transition event.
+quench can be set by the {min} keyword.  Note that typically, you do
+not need to perform a highly-converged minimization to detect a
+transition event.
 
 The event check is performed by a compute with the specified
 {compute-ID}.  Currently there is only one compute that works with the
@@ -135,11 +137,17 @@ event/displace"_compute_event_displace.html checks whether any atom in
 the compute group has moved further than a specified threshold
 distance.  If so, an "event" has occurred.
 
-The neb calculation is similar to that invoked by the "neb"_neb.html
+The NEB calculation is similar to that invoked by the "neb"_neb.html
 command, except that the final state is generated internally, instead
-of being read in from a file. The TAD implementation provides default
+of being read in from a file.  The style of minimization performed by
-values for the NEB settings, which can be overridden using the {neb}
+NEB is determined by the {neb_style} keyword and must be a damped
-and {neb_style} keywords.
+dynamics minimizer.  The tolerances and limits for each NEB
+calculation can be set by the {neb} keyword.  As discussed on the
+"neb"_neb.html, it is often advantageous to use a larger timestep for
+NEB than for normal dyanmics.  Since the size of the timestep set by
+the "timestep"_timestep.html command is used by TAD for performing
+dynamics, there is a {neb_step} keyword which can be used to set a
+larger timestep for each NEB calculation if desired.
 
 :line
 
@@ -201,8 +209,7 @@ while the global event number, energy barrier, and
 in the immediately preceding block of detected events.  
 The low-temperature event time {t_lo} is incremented by {delt_lo}.
 
-
+NEB statistics are written to the file specified by the {neb_log}
-The NEB statistics are written to the file specified by the {neb_log}
 keyword. If the keyword value is "none", then no NEB statistics are
 printed out. The statistics are written every {Nevery} timesteps.  See
 the "neb"_neb.html command for a full description of the NEB
@@ -292,8 +299,8 @@ dt/reset"_fix_dt_reset.html and "fix deposit"_fix_deposit.html.
 [Default:] 
 
 The option defaults are {min} = 0.1 0.1 40 50, {neb} = 0.01 100 100
-10, {min_style} = {cg}, {neb_style} = {quickmin}, and {neb_log} =
+10, {neb_style} = {quickmin}, {neb_step} = the same timestep set by
-"none"
+the "timestep"_timestep.html command, and {neb_log} = "none".
 
 :line