git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@4987 f3b2605a-c512-4ea7-a41b-209d697bcdaa

doc/neb.html

@@ -202,9 +202,21 @@ barrier statistics, thermodynamic output by each replica, dump files,
 and restart files.
 </P>
 <P>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 is
-limited to the potential energy of each replica, printed once every
-<I>Nevery</I> timesteps.
+this case), the print-out to the screen and master log.lammps file
+contains a line of output, printed once every <I>Nevery</I> timesteps.  It
+contains the timestep, the maximum force per replica, the maximum
+force per atom (in any replica), and the 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 <I>ftol</I> 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 "reaction coordinate" (RC) for each
+replica is the length of the 3N-length vector of the distances between
+its atoms and the preceding replica's atoms, added to the RC of the
+preceding replica.  The RC of the first replica = 0.0; the remaining
+RCs are normalized so that the RC of the last replica = 1.0.  In this
+case, N is only the atoms being operated on by the fix neb command.
 </P>
 <P>When running on multiple partitions, LAMMPS produces additional log
 files for each partition, e.g. log.lammps.0, log.lammps.1, etc.  For a

doc/neb.txt

@@ -199,9 +199,21 @@ 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 is
-limited to the potential energy of each replica, printed once every
-{Nevery} timesteps.
+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), and the 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 "reaction coordinate" (RC) for each
+replica is the length of the 3N-length vector of the distances between
+its atoms and the preceding replica's atoms, added to the RC of the
+preceding replica.  The RC of the first replica = 0.0; the remaining
+RCs are normalized so that the RC of the last replica = 1.0.  In this
+case, N is only the atoms being operated on by the fix neb command.
 
 When running on multiple partitions, LAMMPS produces additional log
 files for each partition, e.g. log.lammps.0, log.lammps.1, etc.  For a

doc/variable.html

@@ -358,12 +358,14 @@ the natural log; log() is the base 10 log.
 </P>
 <P>The random() function generates a uniform random number between lo and
 hi.  The normal() function generates a Gaussian variate centered on mu
-with variance sigma.  In both cases the seed is used the first time
+with variance sigma^2.  In both cases the seed is used the first time
 the internal random number generator is invoked, to initialize it.
-For equal-style variables, every processor uses the same seed.  For
-atom-style variables, a new unique seed is created for each processor,
+For equal-style variables, every processor uses the same seed so that
+they each generate the same sequence of random numbers.  For
+atom-style variables, a unique seed is created for each processor,
 based on the specified seed.  This effectively generates a different
-random number for each atom being looped over.
+random number for each atom being looped over in the atom-style
+variable.
 </P>
 <P>The ceil(), floor(), and round() functions are those in the C math
 library.  Ceil() is the smallest integer not less than its argument.

doc/variable.txt

@@ -358,12 +358,14 @@ the natural log; log() is the base 10 log.
 
 The random() function generates a uniform random number between lo and
 hi.  The normal() function generates a Gaussian variate centered on mu
-with variance sigma.  In both cases the seed is used the first time
+with variance sigma^2.  In both cases the seed is used the first time
 the internal random number generator is invoked, to initialize it.
-For equal-style variables, every processor uses the same seed.  For
-atom-style variables, a new unique seed is created for each processor,
+For equal-style variables, every processor uses the same seed so that
+they each generate the same sequence of random numbers.  For
+atom-style variables, a unique seed is created for each processor,
 based on the specified seed.  This effectively generates a different
-random number for each atom being looped over.
+random number for each atom being looped over in the atom-style
+variable.
 
 The ceil(), floor(), and round() functions are those in the C math
 library.  Ceil() is the smallest integer not less than its argument.