git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@373 f3b2605a-c512-4ea7-a41b-209d697bcdaa

doc/create_box.html

@@ -24,14 +24,39 @@
 </PRE>
 <P><B>Description:</B>
 </P>
-<P>This command creates a simulation box that encloses the specified
+<P>This command creates a simulation box based on the specified region.
-region.  Thus a <A HREF = "region.html">region</A> command must first be used to
+Thus a <A HREF = "region.html">region</A> command must first be used to define a
-define a geometric domain.  If the region is not of style <I>block</I>,
+geometric domain.
-LAMMPS encloses it with a rectangular simulation box.
 </P>
 <P>The argument N is the number of atom types that will be used in the
 simulation.
 </P>
+<P>If the region is not of style <I>prism</I>, then LAMMPS encloses the region
+(block, sphere, etc) with an axis-aligned (orthogonal) box which
+becomes the simulation domain.
+</P>
+<P>If the region is of style <I>prism</I>, LAMMPS creates a non-orthogonal
+simulation domain shaped as a parallelepiped with triclinic symmetry.
+See the <A HREF = "region.html">region prism</A> command for a description of how
+the shape of the parallelepiped is defined.  The parallelepiped has
+its "origin" at (xlo,ylo,zlo) and 3 edge vectors starting from its
+origin given by a = (xhi-xlo,0,0); b = (xy,yhi-ylo,0); c =
+(xz,yz,zhi-zlo).
+</P>
+<P>A prism region used with the create_box command must have skew factors
+(xy,xz,yz) that do not skew the box more than half the distance of its
+side lengths.  For example, if ylo = 2 and yhi = 12, then the y box
+length is 10 and the xy factor must be between -5 and 5.  Similary xz
+must be between -(zhi-zlo)/2 and +(zhi-zlo)/2 and yz must be between
+-(zhi-zlo)/2 and +(zhi-zlo)/2.
+</P>
+<P>When a prism region is used, the simulation domain must be periodic in
+any dimensions with a non-zero skew factor, as defined by the
+<A HREF = "boundary.html">boundary</A> command.  I.e. if the xy factor is non-zero,
+then both the x and y dimensions must be periodic.  Similarly, x and z
+must be periodic if xz is non-zero and y and z must be periodic if yz
+is non-zero.
+</P>
 <P><B>Restrictions:</B>
 </P>
 <P>An <A HREF = "atom_style.html">atom_style</A> and <A HREF = "region.html">region</A> must have

doc/create_box.txt

@@ -21,14 +21,39 @@ create_atoms 2 mybox :pre
 
 [Description:]
 
-This command creates a simulation box that encloses the specified
+This command creates a simulation box based on the specified region.
-region.  Thus a "region"_region.html command must first be used to
+Thus a "region"_region.html command must first be used to define a
-define a geometric domain.  If the region is not of style {block},
+geometric domain.
-LAMMPS encloses it with a rectangular simulation box.
 
 The argument N is the number of atom types that will be used in the
 simulation.
 
+If the region is not of style {prism}, then LAMMPS encloses the region
+(block, sphere, etc) with an axis-aligned (orthogonal) box which
+becomes the simulation domain.
+
+If the region is of style {prism}, LAMMPS creates a non-orthogonal
+simulation domain shaped as a parallelepiped with triclinic symmetry.
+See the "region prism"_region.html command for a description of how
+the shape of the parallelepiped is defined.  The parallelepiped has
+its "origin" at (xlo,ylo,zlo) and 3 edge vectors starting from its
+origin given by a = (xhi-xlo,0,0); b = (xy,yhi-ylo,0); c =
+(xz,yz,zhi-zlo).
+
+A prism region used with the create_box command must have skew factors
+(xy,xz,yz) that do not skew the box more than half the distance of its
+side lengths.  For example, if ylo = 2 and yhi = 12, then the y box
+length is 10 and the xy factor must be between -5 and 5.  Similary xz
+must be between -(zhi-zlo)/2 and +(zhi-zlo)/2 and yz must be between
+-(zhi-zlo)/2 and +(zhi-zlo)/2.
+
+When a prism region is used, the simulation domain must be periodic in
+any dimensions with a non-zero skew factor, as defined by the
+"boundary"_boundary.html command.  I.e. if the xy factor is non-zero,
+then both the x and y dimensions must be periodic.  Similarly, x and z
+must be periodic if xz is non-zero and y and z must be periodic if yz
+is non-zero.
+
 [Restrictions:]
 
 An "atom_style"_atom_style.html and "region"_region.html must have

doc/dump.html

@@ -281,6 +281,13 @@ could then be output with these keywords.
 
 <P><B>Restrictions:</B>
 </P>
+<P>Scaled coordinates cannot be writted to dump files when the simulation
+box is triclinic (non-orthogonal).  Note that this is the default for
+dump style <I>atom</I>; the <A HREF = "dump_modify.html">dump_modify command</A> must be
+used to change it.  The exception is DCD files which store the tilt
+factors for subsequent visualization by programs like
+<A HREF = "http://www.ks.uiuc.edu/Research/vmd">VMD</A>.
+</P>
 <P>To write gzipped dump files, you must compile LAMMPS with the -DGZIP
 option - see the <A HREF = "Section_start.html#2_2">Making LAMMPS</A> section of the
 documentation.

doc/dump.txt

@@ -271,6 +271,13 @@ could then be output with these keywords.
 
 [Restrictions:]
 
+Scaled coordinates cannot be writted to dump files when the simulation
+box is triclinic (non-orthogonal).  Note that this is the default for
+dump style {atom}; the "dump_modify command"_dump_modify.html must be
+used to change it.  The exception is DCD files which store the tilt
+factors for subsequent visualization by programs like
+"VMD"_http://www.ks.uiuc.edu/Research/vmd.
+
 To write gzipped dump files, you must compile LAMMPS with the -DGZIP
 option - see the "Making LAMMPS"_Section_start.html#2_2 section of the
 documentation.

doc/fix_wall_gran.html

@@ -79,9 +79,11 @@ also set to the derivative of this expression.
 </P>
 <P><B>Restrictions:</B>
 </P>
-<P>Can only be used if LAMMPS was built with the "granular" package.  A
+<P>Any dimension (xyz) that has a granular wall must be non-periodic.
-zcylinder wall can only be oscillated in the z dimension.  This fix
+</P>
-can only be used with atom_style granular.
+<P>This fix can only be used if LAMMPS was built with the "granular"
+package and with atom_style granular.  A zcylinder wall can only be
+oscillated in the z dimension.
 </P>
 <P><B>Related commands:</B>
 </P>

doc/fix_wall_gran.txt

@@ -69,9 +69,11 @@ also set to the derivative of this expression.
 
 [Restrictions:]
 
-Can only be used if LAMMPS was built with the "granular" package.  A
+Any dimension (xyz) that has a granular wall must be non-periodic.
-zcylinder wall can only be oscillated in the z dimension.  This fix
+
-can only be used with atom_style granular.
+This fix can only be used if LAMMPS was built with the "granular"
+package and with atom_style granular.  A zcylinder wall can only be
+oscillated in the z dimension.
 
 [Related commands:]
 

doc/fix_wall_lj126.html

@@ -56,7 +56,9 @@ want that energy to be included in the total potential energy of the
 system (the quantity being minimized), you must enable the
 <A HREF = "fix_modify.html">fix_modify</A> <I>energy</I> option for this fix.
 </P>
-<P><B>Restrictions:</B> none
+<P><B>Restrictions:</B>
+</P>
+<P>Any dimension (xyz) that has a LJ 12/6 wall must be non-periodic.
 </P>
 <P><B>Related commands:</B>
 </P>

doc/fix_wall_lj126.txt

@@ -53,7 +53,9 @@ want that energy to be included in the total potential energy of the
 system (the quantity being minimized), you must enable the
 "fix_modify"_fix_modify.html {energy} option for this fix.
 
-[Restrictions:] none
+[Restrictions:]
+
+Any dimension (xyz) that has a LJ 12/6 wall must be non-periodic.
 
 [Related commands:]
 

doc/fix_wall_lj93.html

@@ -57,7 +57,9 @@ want that energy to be included in the total potential energy of the
 system (the quantity being minimized), you must enable the
 <A HREF = "fix_modify.html">fix_modify</A> <I>energy</I> option for this fix.
 </P>
-<P><B>Restrictions:</B> none
+<P><B>Restrictions:</B>
+</P>
+<P>Any dimension (xyz) that has a LJ 9/3 wall must be non-periodic.
 </P>
 <P><B>Related commands:</B>
 </P>

doc/fix_wall_lj93.txt

@@ -54,7 +54,9 @@ want that energy to be included in the total potential energy of the
 system (the quantity being minimized), you must enable the
 "fix_modify"_fix_modify.html {energy} option for this fix.
 
-[Restrictions:] none
+[Restrictions:]
+
+Any dimension (xyz) that has a LJ 9/3 wall must be non-periodic.
 
 [Related commands:]
 

doc/fix_wall_reflect.html

@@ -28,10 +28,7 @@ fix walls all wall/reflect xlo ylo zlo xhi yhi zhi
 <P><B>Description:</B>
 </P>
 <P>Bound the simulation with one or more walls which reflect particles
-when they attempt to move thru them.  Normally, the simulation domain
+when they attempt to move thru them. 
-should be set non-periodic via the <A HREF = "boundary.html">boundary</A> command in
-any dimension that has such a wall, but LAMMPS does not check for this
-condition.
 </P>
 <P>Reflection means that if an atom moves outside the box on a timestep
 by a distance delta (e.g. due to <A HREF = "fix_nve.html">fix nve</A>), then it is
@@ -46,7 +43,9 @@ in the input script, since the adjustments it makes to atom
 coordinates should come after the changes made by time integration.
 LAMMPS will warn you if your fixes are not ordered this way.
 </P>
-<P><B>Restrictions:</B> none
+<P><B>Restrictions:</B>
+</P>
+<P>Any dimension (xyz) that has a reflecting wall must be non-periodic.
 </P>
 <P><B>Related commands:</B>
 </P>

doc/fix_wall_reflect.txt

@@ -25,10 +25,7 @@ fix walls all wall/reflect xlo ylo zlo xhi yhi zhi :pre
 [Description:]
 
 Bound the simulation with one or more walls which reflect particles
-when they attempt to move thru them.  Normally, the simulation domain
+when they attempt to move thru them. 
-should be set non-periodic via the "boundary"_boundary.html command in
-any dimension that has such a wall, but LAMMPS does not check for this
-condition.
 
 Reflection means that if an atom moves outside the box on a timestep
 by a distance delta (e.g. due to "fix nve"_fix_nve.html), then it is
@@ -43,7 +40,9 @@ in the input script, since the adjustments it makes to atom
 coordinates should come after the changes made by time integration.
 LAMMPS will warn you if your fixes are not ordered this way.
 
-[Restrictions:] none
+[Restrictions:]
+
+Any dimension (xyz) that has a reflecting wall must be non-periodic.
 
 [Related commands:]
 

doc/lattice.html

@@ -15,7 +15,7 @@
 </P>
 <PRE>lattice style scale keyword values ... 
 </PRE>
-<UL><LI>style = <I>none</I> or <I>sc</I> or <I>bcc</I> or <I>fcc</I> or <I>diamond</I> or         <I>sq</I> or <I>sq2</I> or <I>hex</I> or <I>user</I> 
+<UL><LI>style = <I>none</I> or <I>sc</I> or <I>bcc</I> or <I>fcc</I> or <I>diamond</I> or         <I>sq</I> or <I>sq2</I> or <I>hex</I> or <I>custom</I> 
 
 <LI>scale = scale factor between lattice and simulation box 
 
@@ -27,13 +27,15 @@
 </PRE>
 <LI>zero or more keyword/value pairs may be appended 
 
-<LI>keyword = <I>origin</I> or <I>orient</I> or <I>a1</I> or <I>a2</I> or <I>a3</I> or <I>basis</I> 
+<LI>keyword = <I>origin</I> or <I>orient</I> or <I>spacings</I> or <I>a1</I> or <I>a2</I> or <I>a3</I> or <I>basis</I> 
 
 <PRE>  <I>origin</I> values = x y z
     x,y,z = fractions of a unit cell (0 <= x,y,z < 1)
   <I>orient</I> values = dim i j k
     dim = <I>x</I> or <I>y</I> or <I>z</I>
     i,j,k = integer lattice directions
+  <I>spacing</I> values = dx dy dz
+    dx,dy,dz = lattice spacings in the x,y,z box directions
   <I>a1</I>,<I>a2</I>,<I>a3</I> values = x y z
     x,y,z = primitive vector components that define unit cell
   <I>basis</I> values = x y z
@@ -46,8 +48,8 @@
 <PRE>lattice fcc 3.52
 lattice hex 0.85
 lattice sq 0.8 origin 0.0 0.5 0.0 orient x 1 1 0 orient y -1 1 0
-lattice user 3.52 a1 1.0 0.0 0.0 a2 0.5 1.0 0.0 a3 0.0 0.0 0.5 &
+lattice custom 3.52 a1 1.0 0.0 0.0 a2 0.5 1.0 0.0 a3 0.0 0.0 0.5 &
-                  basis 0.0 0.0 0.0 basis 0.5 0.5 0.5
+                    basis 0.0 0.0 0.0 basis 0.5 0.5 0.5
 lattice none 
 </PRE>
 <P><B>Description:</B>
@@ -71,7 +73,7 @@ underlying problem geometry is atoms on a lattice.
 <P>The lattice style must be consistent with the dimension of the
 simulation - see the <A HREF = "dimension.html">dimension</A> command.  Styles <I>sc</I>
 or <I>bcc</I> or <I>fcc</I> or <I>diamond</I> are for 3d problems.  Styles <I>sq</I> or
-<I>sq2</I> or <I>hex</I> are for 2d problems.  Style <I>user</I> can be used for
+<I>sq2</I> or <I>hex</I> are for 2d problems.  Style <I>custom</I> can be used for
 either 2d or 3d problems.
 </P>
 <P>A lattice consists of a unit cell, a set of basis atoms within that
@@ -103,7 +105,7 @@ corner and one at the center of the square.  A <I>hex</I> style is also a
 and a2 = 0.0 sqrt(3.0) 0.0.  It has 2 basis atoms, one at the corner
 and one at the center of the rectangle.
 </P>
-<P>A lattice of style <I>user</I> allows you to specify a1, a2, a3, and a list
+<P>A lattice of style <I>custom</I> 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
@@ -116,7 +118,7 @@ means a position half-way across the unit cell in that dimension.
 
 <P>This sub-section discusses the arguments that determine how the
 idealized unit cell is transformed into a lattice of points within the
-simulation box with desired spacings.
+simulation box.
 </P>
 <P>The <I>scale</I> argument determines how the size of the unit cell will be
 scaled when mapping it into the simulation box.  I.e. it determines a
@@ -159,17 +161,27 @@ the Z direction.
 <HR>
 
 <P>Several LAMMPS commands have the option to use distance units that are
-inferred from "lattice spacings" in the x,y,z directions.  E.g. the
+inferred from "lattice spacings" in the x,y,z box directions.
-<A HREF = "region.html">region</A> command can create a block of size 10x20x20,
+E.g. the <A HREF = "region.html">region</A> command can create a block of size
-where 10 means 10 lattice spacings in the x direction.
+10x20x20, where 10 means 10 lattice spacings in the x direction.
 </P>
-<P>These lattice spacings are computed by LAMMPS in the following way.  A
+<P>The <I>spacing</I> option sets the 3 lattice spacings directly.  All must
-unit cell of the lattice is mapped into the simulation box (scaled,
+be non-zero (use 1.0 for dz in a 2d simulation).  The specified values
-shifted, rotated), so that it now has (perhaps) a modified shape and
+are multiplied by the multiplicative factor described above that is
-orientation.  The lattice spacing in X is defined as the difference
+associated with the scale factor.  Thus a spacing of 1.0 means one
-between the min/max extent of the x coordinates of the 8 corner points
+unit cell independent of the scale factor.  This option can be useful
-of the modified unit cell.  Similarly, the Y and Z lattice spacings
+if the spacings LAMMPS computes are inconvenient to use in subsequent
-are defined as the min/max of the y and z coordinates.
+commands, which can be the case for non-orthogonal or rotated/scaled
+lattices.
+</P>
+<P>If the <I>spacing</I> 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
+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 min/max of
+the y and z coordinates.
 </P>
 <P>Note that if the unit cell has axis-aligned edges (a1,a2,a3) and is
 not rotated (via the <I>orient</I> keyword), then the lattice spacings in
@@ -180,7 +192,7 @@ factor of 3.0 Angstroms, would have a lattice spacing of 3.0 in x and
 </P>
 <P>For unit cells with a more general shape or when a rotation is
 applied, the lattice spacing is less intuitive.  But regardless, the
-values of the computed lattice spacings are printed by LAMMPS, so
+values of the lattice spacings LAMMPS will use are printed out, so
 their effect in commands that use the spacings should be decipherable.
 </P>
 <HR>
@@ -195,14 +207,14 @@ then generate an error.  No additional arguments need be used with
 
 <P><B>Restrictions:</B>
 </P>
-<P>The <I>a1,a2,a3,basis</I> keywords can only be used with style <I>user</I>.
+<P>The <I>a1,a2,a3,basis</I> keywords can only be used with style <I>custom</I>.
 </P>
 <P>For lattices oriented at an angle or with a non-orthognal unit cell,
 care must be taken when using the <A HREF = "region.html">region</A> and
 <A HREF = "create_atoms.html">create_atoms</A> commands to create a periodic system.
 If the box size is not chosen appropriately, the system may not
-actually be periodic, and atoms may overlap incorretly at the faces of
+actually be periodic, and atoms may overlap incorrectly at the faces
-the simulation box.
+of the simulation box.
 </P>
 <P><B>Related commands:</B>
 </P>

doc/lattice.txt

@@ -13,7 +13,7 @@ lattice command :h3
 lattice style scale keyword values ... :pre
 
 style = {none} or {sc} or {bcc} or {fcc} or {diamond} or \
-        {sq} or {sq2} or {hex} or {user} :ulb,l
+        {sq} or {sq2} or {hex} or {custom} :ulb,l
 scale = scale factor between lattice and simulation box :l
   for style {none}:
     scale is not specified (nor any optional args)
@@ -21,12 +21,14 @@ scale = scale factor between lattice and simulation box :l
     scale = reduced density rho* (for LJ units)
     scale = lattice constant in Angstroms (for real or metal units) :pre
 zero or more keyword/value pairs may be appended :l
-keyword = {origin} or {orient} or {a1} or {a2} or {a3} or {basis} :l
+keyword = {origin} or {orient} or {spacings} or {a1} or {a2} or {a3} or {basis} :l
   {origin} values = x y z
     x,y,z = fractions of a unit cell (0 <= x,y,z < 1)
   {orient} values = dim i j k
     dim = {x} or {y} or {z}
     i,j,k = integer lattice directions
+  {spacing} values = dx dy dz
+    dx,dy,dz = lattice spacings in the x,y,z box directions
   {a1},{a2},{a3} values = x y z
     x,y,z = primitive vector components that define unit cell
   {basis} values = x y z
@@ -38,8 +40,8 @@ keyword = {origin} or {orient} or {a1} or {a2} or {a3} or {basis} :l
 lattice fcc 3.52
 lattice hex 0.85
 lattice sq 0.8 origin 0.0 0.5 0.0 orient x 1 1 0 orient y -1 1 0
-lattice user 3.52 a1 1.0 0.0 0.0 a2 0.5 1.0 0.0 a3 0.0 0.0 0.5 &
+lattice custom 3.52 a1 1.0 0.0 0.0 a2 0.5 1.0 0.0 a3 0.0 0.0 0.5 &
-                  basis 0.0 0.0 0.0 basis 0.5 0.5 0.5
+                    basis 0.0 0.0 0.0 basis 0.5 0.5 0.5
 lattice none :pre
 
 [Description:]
@@ -63,7 +65,7 @@ underlying problem geometry is atoms on a lattice.
 The lattice style must be consistent with the dimension of the
 simulation - see the "dimension"_dimension.html command.  Styles {sc}
 or {bcc} or {fcc} or {diamond} are for 3d problems.  Styles {sq} or
-{sq2} or {hex} are for 2d problems.  Style {user} can be used for
+{sq2} or {hex} are for 2d problems.  Style {custom} can be used for
 either 2d or 3d problems.
 
 A lattice consists of a unit cell, a set of basis atoms within that
@@ -95,7 +97,7 @@ corner and one at the center of the square.  A {hex} style is also a
 and a2 = 0.0 sqrt(3.0) 0.0.  It has 2 basis atoms, one at the corner
 and one at the center of the rectangle.
 
-A lattice of style {user} allows you to specify a1, a2, a3, and a list
+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
@@ -108,7 +110,7 @@ means a position half-way across the unit cell in that dimension.
 
 This sub-section discusses the arguments that determine how the
 idealized unit cell is transformed into a lattice of points within the
-simulation box with desired spacings.
+simulation box.
 
 The {scale} argument determines how the size of the unit cell will be
 scaled when mapping it into the simulation box.  I.e. it determines a
@@ -151,17 +153,27 @@ the Z direction.
 :line
 
 Several LAMMPS commands have the option to use distance units that are
-inferred from "lattice spacings" in the x,y,z directions.  E.g. the
+inferred from "lattice spacings" in the x,y,z box directions.
-"region"_region.html command can create a block of size 10x20x20,
+E.g. the "region"_region.html command can create a block of size
-where 10 means 10 lattice spacings in the x direction.
+10x20x20, where 10 means 10 lattice spacings in the x direction.
 
-These lattice spacings are computed by LAMMPS in the following way.  A
+The {spacing} option sets the 3 lattice spacings directly.  All must
-unit cell of the lattice is mapped into the simulation box (scaled,
+be non-zero (use 1.0 for dz in a 2d simulation).  The specified values
-shifted, rotated), so that it now has (perhaps) a modified shape and
+are multiplied by the multiplicative factor described above that is
-orientation.  The lattice spacing in X is defined as the difference
+associated with the scale factor.  Thus a spacing of 1.0 means one
-between the min/max extent of the x coordinates of the 8 corner points
+unit cell independent of the scale factor.  This option can be useful
-of the modified unit cell.  Similarly, the Y and Z lattice spacings
+if the spacings LAMMPS computes are inconvenient to use in subsequent
-are defined as the min/max of the y and z coordinates.
+commands, which can be the case for non-orthogonal or rotated/scaled
+lattices.
+
+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
+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 min/max of
+the y and z coordinates.
 
 Note that if the unit cell has axis-aligned edges (a1,a2,a3) and is
 not rotated (via the {orient} keyword), then the lattice spacings in
@@ -172,7 +184,7 @@ factor of 3.0 Angstroms, would have a lattice spacing of 3.0 in x and
 
 For unit cells with a more general shape or when a rotation is
 applied, the lattice spacing is less intuitive.  But regardless, the
-values of the computed lattice spacings are printed by LAMMPS, so
+values of the lattice spacings LAMMPS will use are printed out, so
 their effect in commands that use the spacings should be decipherable.
 
 :line
@@ -187,14 +199,14 @@ then generate an error.  No additional arguments need be used with
 
 [Restrictions:]
 
-The {a1,a2,a3,basis} keywords can only be used with style {user}.
+The {a1,a2,a3,basis} keywords can only be used with style {custom}.
 
 For lattices oriented at an angle or with a non-orthognal unit cell,
 care must be taken when using the "region"_region.html and
 "create_atoms"_create_atoms.html commands to create a periodic system.
 If the box size is not chosen appropriately, the system may not
-actually be periodic, and atoms may overlap incorretly at the faces of
+actually be periodic, and atoms may overlap incorrectly at the faces
-the simulation box.
+of the simulation box.
 
 [Related commands:]
 

doc/pair_eam.html

@@ -76,7 +76,7 @@ the DYNAMO <I>funcfl</I> format.  Either single element or alloy systems
 can be modeled using multiple <I>funcfl</I> files and style <I>eam</I>.  For the
 alloy case LAMMPS mixes the single-element potentials to produce alloy
 potentials, the same way that DYNAMO does.  Alternatively, a single
-DYNAMO <I>setfl</I> file of Finnis/Sinclair EAM file can be used by LAMMPS
+DYNAMO <I>setfl</I> file or Finnis/Sinclair EAM file can be used by LAMMPS
 to model alloy systems by invoking the <I>eam/alloy</I> or <I>eam/fs</I> styles
 as described below.  These files require no mixing since they specify
 alloy interactions explicitly.

doc/pair_eam.txt

@@ -68,7 +68,7 @@ the DYNAMO {funcfl} format.  Either single element or alloy systems
 can be modeled using multiple {funcfl} files and style {eam}.  For the
 alloy case LAMMPS mixes the single-element potentials to produce alloy
 potentials, the same way that DYNAMO does.  Alternatively, a single
-DYNAMO {setfl} file of Finnis/Sinclair EAM file can be used by LAMMPS
+DYNAMO {setfl} file or Finnis/Sinclair EAM file can be used by LAMMPS
 to model alloy systems by invoking the {eam/alloy} or {eam/fs} styles
 as described below.  These files require no mixing since they specify
 alloy interactions explicitly.

doc/pair_sw.html

@@ -77,9 +77,11 @@ and three-body coefficients in the formula above:
 <LI>p
 <LI>q 
 </UL>
-<P>The epsilon, sigma, a, A, B, p, and q parameters are for two-body
+<P>The A, B, p, and q parameters are used only for two-body
-interactions.  The lambda, gamma, and costheta0 parameters are for
+interactions.  The lambda, gamma, and costheta0 parameters are used only for
-three-body interactions.  The non-annotated parameters are unitless.
+three-body interactions. The epsilon, sigma and a parameters are used
+for both two-body and three-body interactions.  
+The non-annotated parameters are unitless.
 </P>
 <P>The Stillinger-Weber potential file must contain entries for all the
 elements listed in the pair_coeff command.  It can also contain
@@ -96,13 +98,17 @@ entries would be required, etc.
 <P>As annotated above, the first element in the entry is the center atom
 in a three-body interaction.  Thus an entry for SiCC means a Si atom
 with 2 C atoms as neighbors.  By symmetry, three-body parameters for
-SiCSi and SiSiC entries should be the same.  Two-body parameters for
+SiCSi and SiSiC entries should be the same.   The parameters used for 
-an interaction come from the entry where the 2nd element is repeated.
+the two-body interaction come
-Thus the two-body parameters for Si interacting with C, comes from the
+from the entry where the 2nd element is repeated.  Thus the two-body
-SiCC entry.  Again by symmetry, the two-body parameters in the SiCC
+parameters for Si interacting with C, comes from the SiCC entry.  
-and CSiSi entries should thus be the same.  Two-body parameters in
+Again by symmetry, the two-body parameters in the SiCC
-entries whose 2nd and 3rd element are different (e.g. SiCSi) are
+and CSiSi entries should thus be the same. 
-ignored.
+The parameters used for a particular three-body 
+interaction come from the entry with the corresponding three elements. 
+The parameters used only for two-body interactions (A, B, p, and q) 
+in entries whose 2nd and 3rd element are different (e.g. SiCSi) 
+are not used for anything and can be set to 0.0 if desired.
 </P>
 <P><B>Restrictions:</B>
 </P>

doc/pair_tersoff.html

@@ -79,10 +79,11 @@ above:
 <LI>lambda1 (1/distance units)
 <LI>A (energy units) 
 </UL>
-<P>The n, beta, lambda2, B, R, D, lambda1, and A parameters are for
+<P>The n, beta, lambda2, B, lambda1, and A parameters are only used for
 two-body interactions.  The lambda3, c, d, and costheta0 parameters
-are for three-body interactions.  The non-annotated parameters are
+are only used for three-body interactions. The R and D parameters 
-unitless.
+are used for both two-body and three-body interactions. The 
+non-annotated parameters are unitless.
 </P>
 <P>The Tersoff potential file must contain entries for all the elements
 listed in the pair_coeff command.  It can also contain entries for
@@ -101,12 +102,16 @@ in a three-body interaction and it is bonded to the 2nd atom and the
 bond is influenced by the 3rd atom.  Thus an entry for SiCC means Si
 bonded to a C with another C atom influencing the bond.  Thus
 three-body parameters for SiCSi and SiSiC entries will not, in
-general, be the same.  Two-body parameters for an interaction come
+general, be the same.  The parameters used for the two-body interaction come
 from the entry where the 2nd element is repeated.  Thus the two-body
 parameters for Si interacting with C, comes from the SiCC entry.  By
-symmetry, the two-body parameters in the SiCC and CSiSi entries should
+symmetry, the twobody parameters in the SiCC and CSiSi entries should
-thus be the same.  Two-body parameters in entries whose 2nd and 3rd
+thus be the same.  The parameters used for a particular three-body 
-element are different (e.g. SiCSi) are ignored.
+interaction come from the entry with the corresponding three elements. 
+The parameters used only for two-body interactions 
+(n, beta, lambda2, B, lambda1, and A) 
+in entries whose 2nd and 3rd element are different (e.g. SiCSi) 
+are not used for anything and can be set to 0.0 if desired.
 </P>
 <P><B>Restrictions:</B>
 </P>

doc/read_restart.html

@@ -47,8 +47,8 @@ behavior is wrong.
 </P>
 <P>Because restart files are binary, they may not be portable to other
 machines.  They can be converted to ASCII data files using the
-restart2data tool in the tools sub-directory of the LAMMPS
+<A HREF = "Section_tools.html#restart">restart2data tool</A> in the tools
-distribution.
+sub-directory of the LAMMPS distribution.
 </P>
 <P>Similar to how restart files are written (see the
 <A HREF = "write_restart.html">write_restart</A> and <A HREF = "restart.html">restart</A>
@@ -78,12 +78,14 @@ current LAMMPS simulation.
 <HR>
 
 <P>A restart file stores the units and atom style, simulation box
-attibutes, individual atoms and their attributes including molecular
+attibutes (including whether it is an orthogonal box or a
-topology, force field styles and coefficients,
+non-orthogonal parallelepiped with triclinic symmetry), individual
-<A HREF = "special_bonds.html">special_bonds</A> settings, and atom group
+atoms and their attributes including molecular topology, force field
-definitions.  This means that commands for these quantities do not
+styles and coefficients, <A HREF = "special_bonds.html">special_bonds</A> settings,
-need to be specified in your input script that reads the restart file.
+and atom group definitions.  This means that commands for these
-The exceptions to this are listed below in the Restrictions section.
+quantities do not need to be specified in your input script that reads
+the restart file.  The exceptions to this are listed below in the
+Restrictions section.
 </P>
 <P>Information about the <A HREF = "kspace_style.html">kspace_style</A> settings are
 not stored in the restart file.  Hence if you wish to invoke an Ewald
@@ -120,11 +122,11 @@ bonds will still be broken when the restart file is read.
 </P>
 <P>The <A HREF = "pair_style.html">pair_style</A> <I>eam</I>, <I>table</I>, and <I>hybrid</I> styles
 do not store coefficient data for individual atom type pairs in the
-restart file.  Nor does the <A HREF = "bond_style.html">bond_style</A> <I>hybrid</I>
+restart file.  Nor does the <A HREF = "bond_style.html">bond_style hybrid</A> style
-style.  Thus you must use new <A HREF = "pair_coeff.html">pair_coeff</A> and
+(angle, dihedral hybrid, etc).  Thus for these styles you must use new
-<A HREF = "bond_coeff.html">bond_coeff</A> commands to read the appropriate
+<A HREF = "pair_coeff.html">pair_coeff</A> and <A HREF = "bond_coeff.html">bond_coeff</A> (angle,
-tabulated files or reset the coefficients after the restart file is
+dihedral, etc) commands to read the appropriate tabulated files or
-read.
+reset the coefficients after the restart file is read.
 </P>
 <P><B>Related commands:</B>
 </P>

doc/read_restart.txt

@@ -44,8 +44,8 @@ behavior is wrong.
 
 Because restart files are binary, they may not be portable to other
 machines.  They can be converted to ASCII data files using the
-restart2data tool in the tools sub-directory of the LAMMPS
+"restart2data tool"_Section_tools.html#restart in the tools
-distribution.
+sub-directory of the LAMMPS distribution.
 
 Similar to how restart files are written (see the
 "write_restart"_write_restart.html and "restart"_restart.html
@@ -75,12 +75,14 @@ current LAMMPS simulation.
 :line
 
 A restart file stores the units and atom style, simulation box
-attibutes, individual atoms and their attributes including molecular
+attibutes (including whether it is an orthogonal box or a
-topology, force field styles and coefficients,
+non-orthogonal parallelepiped with triclinic symmetry), individual
-"special_bonds"_special_bonds.html settings, and atom group
+atoms and their attributes including molecular topology, force field
-definitions.  This means that commands for these quantities do not
+styles and coefficients, "special_bonds"_special_bonds.html settings,
-need to be specified in your input script that reads the restart file.
+and atom group definitions.  This means that commands for these
-The exceptions to this are listed below in the Restrictions section.
+quantities do not need to be specified in your input script that reads
+the restart file.  The exceptions to this are listed below in the
+Restrictions section.
 
 Information about the "kspace_style"_kspace_style.html settings are
 not stored in the restart file.  Hence if you wish to invoke an Ewald
@@ -117,11 +119,11 @@ bonds will still be broken when the restart file is read.
 
 The "pair_style"_pair_style.html {eam}, {table}, and {hybrid} styles
 do not store coefficient data for individual atom type pairs in the
-restart file.  Nor does the "bond_style"_bond_style.html {hybrid}
+restart file.  Nor does the "bond_style hybrid"_bond_style.html style
-style.  Thus you must use new "pair_coeff"_pair_coeff.html and
+(angle, dihedral hybrid, etc).  Thus for these styles you must use new
-"bond_coeff"_bond_coeff.html commands to read the appropriate
+"pair_coeff"_pair_coeff.html and "bond_coeff"_bond_coeff.html (angle,
-tabulated files or reset the coefficients after the restart file is
+dihedral, etc) commands to read the appropriate tabulated files or
-read.
+reset the coefficients after the restart file is read.
 
 [Related commands:]
 

doc/region.html

@@ -27,12 +27,11 @@
     c1,c2 = coords of cylinder axis in other 2 dimensions (distance units)
     radius = cylinder radius (distance units)
     lo,hi = bounds of cylinder in dim (distance units)
-  <I>prism</I> args = xlo xhi ylo yhi zlo zhi yxtilt zxtilt zytilt
+  <I>prism</I> args = xlo xhi ylo yhi zlo zhi xy xz yz
-      xlo,xhi,ylo,yhi,zlo,zhi = bounds of untilted prism in all
+      xlo,xhi,ylo,yhi,zlo,zhi = bounds of untilted prism (distance units)
-        dimensions (distance units)
+      xy = distance to skew y in x direction (distance units)
-      yxtilt = distance to shift upper y in x direction (distance units)
+      xz = distance to skew z in x direction (distance units)
-      zxtilt = distance to shift upper z in x direction (distance units)
+      yz = distance to skew z in y direction (distance units)
-      zytilt = distance to shift upper z in y direction (distance units)
   <I>sphere</I> args = x y z radius
       x,y,z = center of sphere (distance units)
       radius = radius of sphere (distance units)
@@ -86,18 +85,21 @@ third example above specifes a cylinder with its axis in the
 y-direction located at x = 2.0 and z = 3.0, with a radius of 5.0, and
 extending in the y-direction from -5.0 to the upper box boundary.
 </P>
-<P>For style <I>prism</I>, a tilted block is defined.  The bounds of the
+<P>For style <I>prism</I>, a parallelepiped is defined (it's too hard to spell
-untilted axis-aligned block are specified in the same way as for the
+parallelepiped in an input script!).  A prism region is used by the
-<I>block</I> style.  A tilt factor for each dimension with respect to
+<A HREF = "create_box.html">create_box</A> command to define a triclinic
-another dimension is also specified.  If the lower xy face of the
+(non-orthogonal) simulation domain.  Think of the parallelepided as
-prism is initially a rectangle (untilted), then the yxtilt factor
+initially an axis-aligned orthogonal box with the same xyz lo/hi
-specifies how far the upper y edge of that face is shifted in the x
+parameters as region style <I>block</I> would define.  Then, while holding
-direction (skewing that face, keeping the xy face a parallelogram).  A
+the (xlo,ylo,zlo) corner point fixed, the box is "skewed" in 3
-plus or minus value can be chosen; 0.0 would be no tilt.  Similarly,
+directions.  First, for the lower xy face of the box, the <I>xy</I> factor
-zxtilt and zytilt describe how far the upper xy face of the prism is
+is how far the upper y edge is shifted in the x direction.  The lower
-translated in the x and y directions to further tilt the prism.  The
+xy face is now a parallelogram.  A plus or minus value for <I>xy</I> can be
-final prism shape remains a parallelipiped, with opposing pairs of the
+specified; 0.0 means no skew.  Then, the upper xy face of the box is
-6 faces remaining parallel to each other.
+translated in the x and y directions by <I>xz</I> and <I>yz</I>.  This results
+in a parallelepiped whose "origin" is at (xlo,ylo,zlo) with 3 edge
+vectors starting from its origin given by a = (xhi-xlo,0,0); b =
+(xy,yhi-ylo,0); c = (xz,yz,zhi-zlo).
 </P>
 <P>The <I>union</I> style creates a region consisting of the volume of all the
 listed regions combined.  The <I>intesect</I> style creates a region
@@ -122,8 +124,8 @@ previously used to define the lattice spacing.
 <P><B>Restrictions:</B> none
 </P>
 <P>A prism cannot be of 0.0 thickness in any dimension; use a small z
-thickness for 2d simulations.  For 2d simulations, the zxtilt and
+thickness for 2d simulations.  For 2d simulations, the xz and yz
-zytilt parameters must be 0.0.
+parameters must be 0.0.
 </P>
 <P><B>Related commands:</B>
 </P>

doc/region.txt

@@ -22,12 +22,11 @@ style = {block} or {cylinder} or {prism} or {sphere} or {union} or {intersect} :
     c1,c2 = coords of cylinder axis in other 2 dimensions (distance units)
     radius = cylinder radius (distance units)
     lo,hi = bounds of cylinder in dim (distance units)
-  {prism} args = xlo xhi ylo yhi zlo zhi yxtilt zxtilt zytilt
+  {prism} args = xlo xhi ylo yhi zlo zhi xy xz yz
-      xlo,xhi,ylo,yhi,zlo,zhi = bounds of untilted prism in all
+      xlo,xhi,ylo,yhi,zlo,zhi = bounds of untilted prism (distance units)
-        dimensions (distance units)
+      xy = distance to skew y in x direction (distance units)
-      yxtilt = distance to shift upper y in x direction (distance units)
+      xz = distance to skew z in x direction (distance units)
-      zxtilt = distance to shift upper z in x direction (distance units)
+      yz = distance to skew z in y direction (distance units)
-      zytilt = distance to shift upper z in y direction (distance units)
   {sphere} args = x y z radius
       x,y,z = center of sphere (distance units)
       radius = radius of sphere (distance units)
@@ -77,18 +76,21 @@ third example above specifes a cylinder with its axis in the
 y-direction located at x = 2.0 and z = 3.0, with a radius of 5.0, and
 extending in the y-direction from -5.0 to the upper box boundary.
 
-For style {prism}, a tilted block is defined.  The bounds of the
+For style {prism}, a parallelepiped is defined (it's too hard to spell
-untilted axis-aligned block are specified in the same way as for the
+parallelepiped in an input script!).  A prism region is used by the
-{block} style.  A tilt factor for each dimension with respect to
+"create_box"_create_box.html command to define a triclinic
-another dimension is also specified.  If the lower xy face of the
+(non-orthogonal) simulation domain.  Think of the parallelepided as
-prism is initially a rectangle (untilted), then the yxtilt factor
+initially an axis-aligned orthogonal box with the same xyz lo/hi
-specifies how far the upper y edge of that face is shifted in the x
+parameters as region style {block} would define.  Then, while holding
-direction (skewing that face, keeping the xy face a parallelogram).  A
+the (xlo,ylo,zlo) corner point fixed, the box is "skewed" in 3
-plus or minus value can be chosen; 0.0 would be no tilt.  Similarly,
+directions.  First, for the lower xy face of the box, the {xy} factor
-zxtilt and zytilt describe how far the upper xy face of the prism is
+is how far the upper y edge is shifted in the x direction.  The lower
-translated in the x and y directions to further tilt the prism.  The
+xy face is now a parallelogram.  A plus or minus value for {xy} can be
-final prism shape remains a parallelipiped, with opposing pairs of the
+specified; 0.0 means no skew.  Then, the upper xy face of the box is
-6 faces remaining parallel to each other.
+translated in the x and y directions by {xz} and {yz}.  This results
+in a parallelepiped whose "origin" is at (xlo,ylo,zlo) with 3 edge
+vectors starting from its origin given by a = (xhi-xlo,0,0); b =
+(xy,yhi-ylo,0); c = (xz,yz,zhi-zlo).
 
 The {union} style creates a region consisting of the volume of all the
 listed regions combined.  The {intesect} style creates a region
@@ -113,8 +115,8 @@ previously used to define the lattice spacing.
 [Restrictions:] none
 
 A prism cannot be of 0.0 thickness in any dimension; use a small z
-thickness for 2d simulations.  For 2d simulations, the zxtilt and
+thickness for 2d simulations.  For 2d simulations, the xz and yz
-zytilt parameters must be 0.0.
+parameters must be 0.0.
 
 [Related commands:]
 

doc/thermo_style.html

@@ -43,7 +43,7 @@
       enthalpy = enthalpy (pe + press*vol)
       evdwl = VanderWaal pairwise energy
       ecoul = Coulombic pairwise energy
-      epair = pairwise energy (evdwl + ecoul)
+      epair = pairwise energy (evdwl + ecoul + elong + etail)
       ebond = bond energy
       eangle = angle energy
       edihed = dihedral energy

doc/thermo_style.txt

@@ -38,7 +38,7 @@ args = list of arguments for a particular style :l
       enthalpy = enthalpy (pe + press*vol)
       evdwl = VanderWaal pairwise energy
       ecoul = Coulombic pairwise energy
-      epair = pairwise energy (evdwl + ecoul)
+      epair = pairwise energy (evdwl + ecoul + elong + etail)
       ebond = bond energy
       eangle = angle energy
       edihed = dihedral energy