diff -Naur lammps-14Apr08/doc/lattice.html lammps-15Apr08/doc/lattice.html --- lammps-14Apr08/doc/lattice.html 2008-04-11 14:09:19.000000000 -0600 +++ lammps-15Apr08/doc/lattice.html 2008-04-14 15:37:50.000000000 -0600 @@ -109,13 +109,13 @@ rectangle.

A lattice of style custom allows you to specify a1, a2, a3, and a -list of basis atoms to put in the unit cell. By default, a1,a2,a3 are -3 orthogonal unit vectors (edges of a unit cube). But you can specify -them to be of any length and non-orthogonal to each other, so that -they describe a tilted parallelepiped. Via the basis keyword you -add atoms, one at a time, to the unit cell. Its arguments are -fractional coordinates (0.0 <= x,y,z < 1.0), so that a value of 0.5 -means a position half-way across the unit cell in that dimension. +list of basis atoms to put in the unit cell. By default, a1 and a2 +and a3 are 3 orthogonal unit vectors (edges of a unit cube). But you +can specify them to be of any length and non-orthogonal to each other, +so that they describe a tilted parallelepiped. Via the basis +keyword you add atoms, one at a time, to the unit cell. Its arguments +are fractional coordinates (0.0 <= x,y,z < 1.0), so that a value of +0.5 means a position half-way across the unit cell in that dimension.

@@ -160,7 +160,7 @@ direction. The 3 lattice directions you specify must be mutually orthogonal and obey the right-hand rule, i.e. (X cross Y) points in the Z direction. Note that this description is really only valid for -orthogonal lattices. if you are using the more general lattice style +orthogonal lattices. If you are using the more general lattice style custom with non-orthogonal a1,a2,a3 vectors, then think of the 3 orient options as creating a 3x3 rotation matrix which is applied to a1,a2,a3 to rotate the original unit cell to a new orientation in the @@ -185,7 +185,7 @@

If the spacing option is not specified, the lattice spacings are computed by LAMMPS in the following way. A unit cell of the lattice is mapped into the simulation box (scaled, shifted, rotated), so that -it now has (perhaps) a modified shape and orientation. The lattice +it now has (perhaps) a modified size and orientation. The lattice spacing in X is defined as the difference between the min/max extent of the x coordinates of the 8 corner points of the modified unit cell. Similarly, the Y and Z lattice spacings are defined as the difference @@ -237,7 +237,7 @@ 

lattice none

For other lattice styles, the option defaults are origin = 0.0 0.0 -0.0, orient = x 1 0 0, orient = y 0 1 0, orient = z 0 0 1, a1 = 1.0 -0.0 0.0, a2 = 0.0 1.0 0.0, and a3 = 0.0 0.0 1.0. +0.0, orient = x 1 0 0, orient = y 0 1 0, orient = z 0 0 1, a1 = 1 0 0, +a2 = 0 1 0, and a3 = 0 0 1.

diff -Naur lammps-14Apr08/doc/lattice.txt lammps-15Apr08/doc/lattice.txt --- lammps-14Apr08/doc/lattice.txt 2008-04-11 14:09:19.000000000 -0600 +++ lammps-15Apr08/doc/lattice.txt 2008-04-14 15:37:50.000000000 -0600 @@ -101,13 +101,13 @@ rectangle. A lattice of style {custom} allows you to specify a1, a2, a3, and a -list of basis atoms to put in the unit cell. By default, a1,a2,a3 are -3 orthogonal unit vectors (edges of a unit cube). But you can specify -them to be of any length and non-orthogonal to each other, so that -they describe a tilted parallelepiped. Via the {basis} keyword you -add atoms, one at a time, to the unit cell. Its arguments are -fractional coordinates (0.0 <= x,y,z < 1.0), so that a value of 0.5 -means a position half-way across the unit cell in that dimension. +list of basis atoms to put in the unit cell. By default, a1 and a2 +and a3 are 3 orthogonal unit vectors (edges of a unit cube). But you +can specify them to be of any length and non-orthogonal to each other, +so that they describe a tilted parallelepiped. Via the {basis} +keyword you add atoms, one at a time, to the unit cell. Its arguments +are fractional coordinates (0.0 <= x,y,z < 1.0), so that a value of +0.5 means a position half-way across the unit cell in that dimension. :line @@ -152,7 +152,7 @@ direction. The 3 lattice directions you specify must be mutually orthogonal and obey the right-hand rule, i.e. (X cross Y) points in the Z direction. Note that this description is really only valid for -orthogonal lattices. if you are using the more general lattice style +orthogonal lattices. If you are using the more general lattice style {custom} with non-orthogonal a1,a2,a3 vectors, then think of the 3 {orient} options as creating a 3x3 rotation matrix which is applied to a1,a2,a3 to rotate the original unit cell to a new orientation in the @@ -177,7 +177,7 @@ If the {spacing} option is not specified, the lattice spacings are computed by LAMMPS in the following way. A unit cell of the lattice is mapped into the simulation box (scaled, shifted, rotated), so that -it now has (perhaps) a modified shape and orientation. The lattice +it now has (perhaps) a modified size and orientation. The lattice spacing in X is defined as the difference between the min/max extent of the x coordinates of the 8 corner points of the modified unit cell. Similarly, the Y and Z lattice spacings are defined as the difference @@ -229,5 +229,5 @@ lattice none :pre For other lattice styles, the option defaults are origin = 0.0 0.0 -0.0, orient = x 1 0 0, orient = y 0 1 0, orient = z 0 0 1, a1 = 1.0 -0.0 0.0, a2 = 0.0 1.0 0.0, and a3 = 0.0 0.0 1.0. +0.0, orient = x 1 0 0, orient = y 0 1 0, orient = z 0 0 1, a1 = 1 0 0, +a2 = 0 1 0, and a3 = 0 0 1. diff -Naur lammps-14Apr08/doc/min_modify.html lammps-15Apr08/doc/min_modify.html --- lammps-14Apr08/doc/min_modify.html 2008-02-29 18:13:20.000000000 -0700 +++ lammps-15Apr08/doc/min_modify.html 2008-04-14 15:37:10.000000000 -0600 @@ -17,48 +17,32 @@

Examples:

-
min_modify linestyle scan dmin 0.001 dmax 0.2
-min_modify lineiter 5 
+
min_modify dmax 0.2 
 

 
Description:
 

-
This command sets parameters that affect the minimization algorithms.
-The various settings may effect the convergence rate and overall
-number of force evaluations required by a minimization, so users can
-experiment with these parameters to tune their minimizations.
-

-
The linestyle sets the algorithm used for 1d line searches at each
-outer iteration of the minimizer.  The secant style uses two
-successive force/energy evaluations to create a parabola and pick its
-minimum as an estimate of the next iteration's 1d minimum.  The scan
-style starts its 1d search at dmin and doubles the distance along
-the line at which the energy is computed until the minimum is passed.
-It continues only as far as dmax.  Normally, the secant method
-should find more accurate 1d minimums in less iterations, but the
-scan method can be more robust.
-

-
The dmin and dmax settings are both used by the scan line search
-as described above.  For the secant line search, only the dmin
-value is used to pick an initial point to begin the secant
-approximation.
-

-
The lineiter setting is used by the secant algorithm to limit its
-iterations.  The smaller the setting, the more inaccurate the line
-search becomes.  Nonlinear conjugate gradient is not thought to
-require high-accuracy line searches in order to converge efficiently.
+
This command sets parameters that affect the energy minimization
+algorithms.  The various settings may effect the convergence rate and
+overall number of force evaluations required by a minimization, so
+users can experiment with these parameters to tune their
+minimizations.
+

+
The minimization algorithms have an outer iteration (conjugate
+gradient or steepest descent) 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
+distance units means no atom will move further than 0.1 Angstroms in a
+single outer iteration.  This is typically set to avoid the
+possibility than one atom will be moved through another due to strong
+overlapping forces.
 

 
Restrictions: none
 

@@ -68,7 +52,6 @@
 

 
Default:
 

-
The option defaults are linestyle = secant, dmin = 1.0e-5, dmax = 0.1,
-and lineiter = 10.
+
The option defaults are dmax = 0.1.
 

 
diff -Naur lammps-14Apr08/doc/min_modify.txt lammps-15Apr08/doc/min_modify.txt
--- lammps-14Apr08/doc/min_modify.txt	2008-02-29 18:13:20.000000000 -0700
+++ lammps-15Apr08/doc/min_modify.txt	2008-04-14 15:37:10.000000000 -0600
@@ -13,47 +13,32 @@
 min_modify keyword values ... :pre
 
 one or more keyword/value pairs may be listed :ulb,l
-keyword = {linestyle} or {dmin} or {dmax} or {lineiter}
-  {linestyle} value = {secant} or {scan}
-  {dmin} value = min
-    min = minimum distance for line search to move (distance units)
+keyword = {dmax}
   {dmax} value = max
     max = maximum distance for line search to move (distance units)
-  {lineiter} value = N
-    N = max number of iterations in a line search :pre
 :ule
 
 [Examples:]
 
-min_modify linestyle scan dmin 0.001 dmax 0.2
-min_modify lineiter 5 :pre
+min_modify dmax 0.2 :pre
 
 [Description:]
 
-This command sets parameters that affect the minimization algorithms.
-The various settings may effect the convergence rate and overall
-number of force evaluations required by a minimization, so users can
-experiment with these parameters to tune their minimizations.
-
-The {linestyle} sets the algorithm used for 1d line searches at each
-outer iteration of the minimizer.  The {secant} style uses two
-successive force/energy evaluations to create a parabola and pick its
-minimum as an estimate of the next iteration's 1d minimum.  The {scan}
-style starts its 1d search at {dmin} and doubles the distance along
-the line at which the energy is computed until the minimum is passed.
-It continues only as far as {dmax}.  Normally, the {secant} method
-should find more accurate 1d minimums in less iterations, but the
-{scan} method can be more robust.
-
-The {dmin} and {dmax} settings are both used by the {scan} line search
-as described above.  For the {secant} line search, only the {dmin}
-value is used to pick an initial point to begin the secant
-approximation.
-
-The {lineiter} setting is used by the {secant} algorithm to limit its
-iterations.  The smaller the setting, the more inaccurate the line
-search becomes.  Nonlinear conjugate gradient is not thought to
-require high-accuracy line searches in order to converge efficiently.
+This command sets parameters that affect the energy minimization
+algorithms.  The various settings may effect the convergence rate and
+overall number of force evaluations required by a minimization, so
+users can experiment with these parameters to tune their
+minimizations.
+
+The minimization algorithms have an outer iteration (conjugate
+gradient or steepest descent) 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
+distance units means no atom will move further than 0.1 Angstroms in a
+single outer iteration.  This is typically set to avoid the
+possibility than one atom will be moved through another due to strong
+overlapping forces.
 
 [Restrictions:] none
 
@@ -63,5 +48,4 @@
 
 [Default:]
 
-The option defaults are linestyle = secant, dmin = 1.0e-5, dmax = 0.1,
-and lineiter = 10.
+The option defaults are dmax = 0.1.
diff -Naur lammps-14Apr08/doc/min_style.html lammps-15Apr08/doc/min_style.html
--- lammps-14Apr08/doc/min_style.html	2006-09-21 10:22:34.000000000 -0600
+++ lammps-15Apr08/doc/min_style.html	2008-04-14 15:37:10.000000000 -0600
@@ -15,7 +15,7 @@
 

 
min_style style 
 

-