git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@5017 f3b2605a-c512-4ea7-a41b-209d697bcdaa

doc/dump.html

@@ -137,17 +137,50 @@ LAMMPS <A HREF = "Section_tools.html">post-processing tools</A>, including
 this format.  
 </P>
 <P>For post-processing purposes the <I>atom</I> and <I>custom</I> text files are
-self-describing in the following sense.  The simulation box bounds are
+self-describing in the following sense.
-included in each snapshot and if the box is triclinic
+</P>
-(non-orthogonal), then the tilt factors are also printed; see the
+<P>The simulation box bounds are included in each snapshot.  For
-<A HREF = "region.html">region prism</A> command for a description of tilt factors.
+orthogonal boxes this is formatted as:
-For triclinic boxes the box bounds themselves (first 2 quantities on
+</P>
-each line) are a true "bounding box" around the simulation domain,
+<PRE>ITEM: BOX BOUNDS
-which means they include the effect of any tilt.  The "ITEM: ATOMS"
+xlo xhi
-line in each snapshot also lists the meaning of each column of the
+ylo yhi
-per-atom lines that follow.  For example, this would be "id type xs ys
+zlo zhi 
-zs" for the default <I>atom</I> style, and it will be the atom attributes
+</PRE>
-you specify in the dump command for the <I>custom</I> style.
+<P>where xlo,xhi are the bounds of the simulation box in the x-dimension,
+and similarly for y and z.
+</P>
+<P>For triclinic boxes (non-orthogonal), the tilt factors are also
+included, as a 3rd value on each line:
+</P>
+<PRE>ITEM: BOX BOUNDS xy xz yz
+xlo_bound xhi_bound xy
+ylo_bound yhi_bound xz
+zlo_bound zhi_bound yz 
+</PRE>
+<P>See the <A HREF = "region.html">region prism</A> or <A HREF = "read_data.html">read_data</A>
+commands for a description of tilt factors in LAMMPS, and their
+relationship to other nomenclatures for triclinic geometries,
+e.g. using 3 lattice constants <I>a</I>, <I>b</I>, and <I>c</I>, and 3 angles
+<I>alpha</I>, <I>beta</I> and <I>gamma</I>.
+</P>
+<P>IMPORTANT NOTE: As noted above, for triclinic simulation boxes, the 6
+box bounds (xlo,xhi,ylo,yhi,zlo,zhi) are actually written to the dump
+file as a "bounding box" around the simulation domain, which means
+they include the effect of any tilt, which is convenient for many
+visualization programs.  The bounding box is calculated as follows:
+</P>
+<PRE>xlo_bound = MIN(xlo,xlo+xy,xlo+xz,xlo+xy+xz)
+xhi_bound = MAX(xhi,xhi+xy,xhi+xz,xhi+xy+xz)
+ylo_bound = MIN(ylo,ylo+yz)
+yhi_bound = MAX(yhi,yhi+yz)
+zlo_bound = zlo
+zhi_bound = zhi 
+</PRE>
+<P>The "ITEM: ATOMS" line in each snapshot lists column descriptors for
+the per-atom lines that follow.  For example, the descriptors would be
+"id type xs ys zs" for the default <I>atom</I> style, and would be the atom
+attributes you specify in the dump command for the <I>custom</I> style.
 </P>
 <P>For style <I>atom</I>, atom coordinates are written to the file, along with
 the atom ID and atom type.  By default, atom coords are written in a

doc/dump.txt

@@ -127,17 +127,50 @@ LAMMPS "post-processing tools"_Section_tools.html, including
 this format.  
 
 For post-processing purposes the {atom} and {custom} text files are
-self-describing in the following sense.  The simulation box bounds are
+self-describing in the following sense.
-included in each snapshot and if the box is triclinic
+
-(non-orthogonal), then the tilt factors are also printed; see the
+The simulation box bounds are included in each snapshot.  For
-"region prism"_region.html command for a description of tilt factors.
+orthogonal boxes this is formatted as:
-For triclinic boxes the box bounds themselves (first 2 quantities on
+
-each line) are a true "bounding box" around the simulation domain,
+ITEM: BOX BOUNDS
-which means they include the effect of any tilt.  The "ITEM: ATOMS"
+xlo xhi
-line in each snapshot also lists the meaning of each column of the
+ylo yhi
-per-atom lines that follow.  For example, this would be "id type xs ys
+zlo zhi :pre
-zs" for the default {atom} style, and it will be the atom attributes
+
-you specify in the dump command for the {custom} style.
+where xlo,xhi are the bounds of the simulation box in the x-dimension,
+and similarly for y and z.
+
+For triclinic boxes (non-orthogonal), the tilt factors are also
+included, as a 3rd value on each line:
+
+ITEM: BOX BOUNDS xy xz yz
+xlo_bound xhi_bound xy
+ylo_bound yhi_bound xz
+zlo_bound zhi_bound yz :pre
+
+See the "region prism"_region.html or "read_data"_read_data.html
+commands for a description of tilt factors in LAMMPS, and their
+relationship to other nomenclatures for triclinic geometries,
+e.g. using 3 lattice constants {a}, {b}, and {c}, and 3 angles
+{alpha}, {beta} and {gamma}.
+
+IMPORTANT NOTE: As noted above, for triclinic simulation boxes, the 6
+box bounds (xlo,xhi,ylo,yhi,zlo,zhi) are actually written to the dump
+file as a "bounding box" around the simulation domain, which means
+they include the effect of any tilt, which is convenient for many
+visualization programs.  The bounding box is calculated as follows:
+
+xlo_bound = MIN(xlo,xlo+xy,xlo+xz,xlo+xy+xz)
+xhi_bound = MAX(xhi,xhi+xy,xhi+xz,xhi+xy+xz)
+ylo_bound = MIN(ylo,ylo+yz)
+yhi_bound = MAX(yhi,yhi+yz)
+zlo_bound = zlo
+zhi_bound = zhi :pre
+
+The "ITEM: ATOMS" line in each snapshot lists column descriptors for
+the per-atom lines that follow.  For example, the descriptors would be
+"id type xs ys zs" for the default {atom} style, and would be the atom
+attributes you specify in the dump command for the {custom} style.
 
 For style {atom}, atom coordinates are written to the file, along with
 the atom ID and atom type.  By default, atom coords are written in a

doc/read_data.html

@@ -109,8 +109,8 @@ since if the maximum tilt factor is 5 (as in this example), then
 configurations with tilt = ..., -15, -5, 5, 15, 25, ... are all
 equivalent.
 </P>
-<P>Many crystal structures are defined using three lattice constants <I>a</I>,
+<P>Crystal structures are often defined using three lattice constants
-<I>b</I>, and <I>c</I>, and three angles <I>alpha</I>, <I>beta</I> and <I>gamma</I>. The
+<I>a</I>, <I>b</I>, and <I>c</I>, and three angles <I>alpha</I>, <I>beta</I> and <I>gamma</I>. The
 relationships between these quantities and the LAMMPS box dimensions
 (lx,ly,lz) = (xhi-xlo,yhi-ylo,zhi-zlo) and tilt factors (xy,xz,yz) are
 as follows:

doc/read_data.txt

@@ -106,8 +106,8 @@ since if the maximum tilt factor is 5 (as in this example), then
 configurations with tilt = ..., -15, -5, 5, 15, 25, ... are all
 equivalent.
 
-Many crystal structures are defined using three lattice constants {a},
+Crystal structures are often defined using three lattice constants
-{b}, and {c}, and three angles {alpha}, {beta} and {gamma}. The
+{a}, {b}, and {c}, and three angles {alpha}, {beta} and {gamma}. The
 relationships between these quantities and the LAMMPS box dimensions
 (lx,ly,lz) = (xhi-xlo,yhi-ylo,zhi-zlo) and tilt factors (xy,xz,yz) are
 as follows:

doc/region.html

@@ -85,11 +85,13 @@ region 2 sphere 0.0 0.0 0.0 5 side out wiggle 1 1 0 10
 </P>
 <P>This command defines a geometric region of space.  Various other
 commands use regions.  For example, the region can be filled with
-atoms via the <A HREF = "create_atoms.html">create_atoms</A> command.  Or the atoms
+atoms via the <A HREF = "create_atoms.html">create_atoms</A> command.  Or a bounding
-in the region can be identified as a group via the <A HREF = "group.html">group</A>
+box around the region, can be used to define the simulation box via
-command, or deleted via the <A HREF = "delete_atoms.html">delete_atoms</A> command.
+the <A HREF = "create_box.html">create_box</A> command.  Or the atoms in the region
-Or the surface of the region can be used as a boundary wall via the
+can be identified as a group via the <A HREF = "group.html">group</A> command, or
-<A HREF = "fix_wall_region.html">fix wall/region</A> command.
+deleted via the <A HREF = "delete_atoms.html">delete_atoms</A> command.  Or the
+surface of the region can be used as a boundary wall via the <A HREF = "fix_wall_region.html">fix
+wall/region</A> command.
 </P>
 <P>Normally, regions in LAMMPS are "static", meaning their geometric
 extent does not change with time.  If the <I>vel</I> or <I>wiggle</I> or
@@ -162,6 +164,13 @@ 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>Crystal structures are often defined using three lattice constants
+<I>a</I>, <I>b</I>, and <I>c</I>, and three angles <I>alpha</I>, <I>beta</I> and <I>gamma</I>. The
+relationships between these quantities and a prism with (lx,ly,lz) =
+(xhi-xlo,yhi-ylo,zhi-zlo) and tilt factors (xy,xz,yz) are as follows:
+</P>
+<CENTER><IMG SRC = "Eqs/box.jpg">
+</CENTER>
 <P>A prism region used with the <A HREF = "create_box.html">create_box</A> command must
 have tilt factors (xy,xz,yz) that do not skew the box more than half
 the distance of the parallel box length.  For example, if xlo = 2 and

doc/region.txt

@@ -76,11 +76,13 @@ region 2 sphere 0.0 0.0 0.0 5 side out wiggle 1 1 0 10 :pre
 
 This command defines a geometric region of space.  Various other
 commands use regions.  For example, the region can be filled with
-atoms via the "create_atoms"_create_atoms.html command.  Or the atoms
+atoms via the "create_atoms"_create_atoms.html command.  Or a bounding
-in the region can be identified as a group via the "group"_group.html
+box around the region, can be used to define the simulation box via
-command, or deleted via the "delete_atoms"_delete_atoms.html command.
+the "create_box"_create_box.html command.  Or the atoms in the region
-Or the surface of the region can be used as a boundary wall via the
+can be identified as a group via the "group"_group.html command, or
-"fix wall/region"_fix_wall_region.html command.
+deleted via the "delete_atoms"_delete_atoms.html command.  Or the
+surface of the region can be used as a boundary wall via the "fix
+wall/region"_fix_wall_region.html command.
 
 Normally, regions in LAMMPS are "static", meaning their geometric
 extent does not change with time.  If the {vel} or {wiggle} or
@@ -153,6 +155,13 @@ 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).
 
+Crystal structures are often defined using three lattice constants
+{a}, {b}, and {c}, and three angles {alpha}, {beta} and {gamma}. The
+relationships between these quantities and a prism with (lx,ly,lz) =
+(xhi-xlo,yhi-ylo,zhi-zlo) and tilt factors (xy,xz,yz) are as follows:
+
+:c,image(Eqs/box.jpg) 
+
 A prism region used with the "create_box"_create_box.html command must
 have tilt factors (xy,xz,yz) that do not skew the box more than half
 the distance of the parallel box length.  For example, if xlo = 2 and