git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@7690 f3b2605a-c512-4ea7-a41b-209d697bcdaa

doc/Section_howto.html

@@ -770,19 +770,29 @@ where lx = xhi-xlo, and similarly in the y and z dimensions.  The 6
 parameters, as well as lx,ly,lz, can be output via the <A HREF = "thermo_style.html">thermo_style
 custom</A> command.
 </P>
-<P>LAMMPS also allows simulations to be perfored in non-orthogonal
+<P>LAMMPS also allows simulations to be perfored in triclinic
-simulation boxes shaped as a parallelepiped with triclinic symmetry.
+(non-orthogonal) simulation boxes shaped as a parallelepiped with
-The parallelepiped has its "origin" at (xlo,ylo,zlo) and is defined by
+triclinic symmetry.  The parallelepiped has its "origin" at
-3 edge vectors starting from the origin given by <B>a</B> = (xhi-xlo,0,0); <B>b</B>
+(xlo,ylo,zlo) and is defined by 3 edge vectors starting from the
-= (xy,yhi-ylo,0); <B>c</B> = (xz,yz,zhi-zlo).  <I>Xy,xz,yz</I> can be 0.0 or
+origin given by <B>a</B> = (xhi-xlo,0,0); <B>b</B> = (xy,yhi-ylo,0); <B>c</B> =
-positive or negative values and are called "tilt factors" because they
+(xz,yz,zhi-zlo).  <I>Xy,xz,yz</I> can be 0.0 or positive or negative values
-are the amount of displacement applied to faces of an originally
+and are called "tilt factors" because they are the amount of
-orthogonal box to transform it into the parallelepiped.  Note that in
+displacement applied to faces of an originally orthogonal box to
-LAMMPS the triclinic simulation box edge vectors <B>a</B>, <B>b</B>, and <B>c</B> cannot be
+transform it into the parallelepiped.  Note that in LAMMPS the
-arbitrary vectors.  As indicated, <B>a</B> must be aligned with the x axis, <B>b</B>
+triclinic simulation box edge vectors <B>a</B>, <B>b</B>, and <B>c</B> cannot be
-must be in the xy plane, and <B>c</B> is arbitrary.  However, this is not a
+arbitrary vectors.  As indicated, <B>a</B> must be aligned with the x axis,
-restriction since it is possible to rotate any set of 3 crystal basis
+<B>b</B> must be in the xy plane, and <B>c</B> is arbitrary.  However, this is
-vectors so that they meet this restriction.
+not a restriction since it is possible to rotate any set of 3 crystal
+basis vectors so that they meet this restriction.
+</P>
+<P>There is no requirement that a triclinic box be periodic in any
+dimension, though it typically should be in at least the 2nd dimension
+of the tilt (y in xy) if you want to enforce a shift in periodic
+boundary conditions across that boundary.  Some commands that work
+with triclinic boxes, e.g. the <A HREF = "fix_deform.html">fix deform</A> and <A HREF = "fix_nh.html">fix
+npt</A> commands, require periodicity or non-shrink-wrap
+boundary conditions in specific dimensions.  See the command doc pages
+for details.
 </P>
 <P>The 9 parameters (xlo,xhi,ylo,yhi,zlo,zhi,xy,xz,yz) are defined at the
 time the simluation box is created.  This happens in one of 3 ways.

doc/Section_howto.txt

@@ -761,19 +761,29 @@ where lx = xhi-xlo, and similarly in the y and z dimensions.  The 6
 parameters, as well as lx,ly,lz, can be output via the "thermo_style
 custom"_thermo_style.html command.
 
-LAMMPS also allows simulations to be perfored in non-orthogonal
+LAMMPS also allows simulations to be perfored in triclinic
-simulation boxes shaped as a parallelepiped with triclinic symmetry.
+(non-orthogonal) simulation boxes shaped as a parallelepiped with
-The parallelepiped has its "origin" at (xlo,ylo,zlo) and is defined by
+triclinic symmetry.  The parallelepiped has its "origin" at
-3 edge vectors starting from the origin given by [a] = (xhi-xlo,0,0); [b]
+(xlo,ylo,zlo) and is defined by 3 edge vectors starting from the
-= (xy,yhi-ylo,0); [c] = (xz,yz,zhi-zlo).  {Xy,xz,yz} can be 0.0 or
+origin given by [a] = (xhi-xlo,0,0); [b] = (xy,yhi-ylo,0); [c] =
-positive or negative values and are called "tilt factors" because they
+(xz,yz,zhi-zlo).  {Xy,xz,yz} can be 0.0 or positive or negative values
-are the amount of displacement applied to faces of an originally
+and are called "tilt factors" because they are the amount of
-orthogonal box to transform it into the parallelepiped.  Note that in
+displacement applied to faces of an originally orthogonal box to
-LAMMPS the triclinic simulation box edge vectors [a], [b], and [c] cannot be
+transform it into the parallelepiped.  Note that in LAMMPS the
-arbitrary vectors.  As indicated, [a] must be aligned with the x axis, [b]
+triclinic simulation box edge vectors [a], [b], and [c] cannot be
-must be in the xy plane, and [c] is arbitrary.  However, this is not a
+arbitrary vectors.  As indicated, [a] must be aligned with the x axis,
-restriction since it is possible to rotate any set of 3 crystal basis
+[b] must be in the xy plane, and [c] is arbitrary.  However, this is
-vectors so that they meet this restriction.
+not a restriction since it is possible to rotate any set of 3 crystal
+basis vectors so that they meet this restriction.
+
+There is no requirement that a triclinic box be periodic in any
+dimension, though it typically should be in at least the 2nd dimension
+of the tilt (y in xy) if you want to enforce a shift in periodic
+boundary conditions across that boundary.  Some commands that work
+with triclinic boxes, e.g. the "fix deform"_fix_deform.html and "fix
+npt"_fix_nh.html commands, require periodicity or non-shrink-wrap
+boundary conditions in specific dimensions.  See the command doc pages
+for details.
 
 The 9 parameters (xlo,xhi,ylo,yhi,zlo,zhi,xy,xz,yz) are defined at the
 time the simluation box is created.  This happens in one of 3 ways.

doc/fix_nh.html

@@ -292,9 +292,9 @@ scale keywords to <I>no</I>.
 <I>xz</I>, <I>yz</I> can sometimes result in arbitrarily large values of the
 tilt dimensions, i.e. a dramatically deformed simulation box.  LAMMPS
 allows the tilt factors to grow a little beyond the normal limit of
-half the box length (0.6 times the box length), and then performs
+half the box length (0.6 times the box length), and then performs a
-flipping or re-shaping to an equivalent periodic cell. The re-shaping
+box "flip" to an equivalent periodic cell. The flip operation is
-operation is described in more detail in the doc page for <A HREF = "fix_deform.html">fix
+described in more detail in the doc page for <A HREF = "fix_deform.html">fix
 deform</A>.  Both the barostat dynamics and the atom
 trajectories are unaffected by this operation.  However, if a tilt
 factor is incremented by a large amount (1.5 times the box length) on
@@ -310,6 +310,13 @@ equilibrium liquids can not support a shear stress and that
 equilibrium solids can not support shear stresses that exceed the
 yield stress.
 </P>
+<P>The one exception to this rule is if the 1st dimension in the tilt
+factor (x for xy) is non-periodic.  In that case, the limits on the
+tilt factor are not enforced, since flipping the box in that dimension
+does not change the atom positions due to non-periodicity.  In this
+mode, if you tilt the system to extreme angles, the simulation will
+simply become inefficient due to the highly skewed simulation box.
+</P>
 <P>IMPORTANT NOTE: Unlike the <A HREF = "fix_temp_berendsen.html">fix
 temp/berendsen</A> command which performs
 thermostatting but NO time integration, these fixes perform
@@ -514,7 +521,8 @@ and if the tilt factor is not coupled to the barostat via keywords
 </P>
 <P><B>Related commands:</B>
 </P>
-<P><A HREF = "fix_nve.html">fix nve</A>, <A HREF = "fix_modify.html">fix_modify</A>, <A HREF = "run_style.html">run_style</A>
+<P><A HREF = "fix_nve.html">fix nve</A>, <A HREF = "fix_modify.html">fix_modify</A>,
+<A HREF = "run_style.html">run_style</A>
 </P>
 <P><B>Default:</B>
 </P>

doc/fix_nh.txt

@@ -282,9 +282,9 @@ IMPORTANT NOTE: Using a barostat coupled to tilt dimensions {xy},
 {xz}, {yz} can sometimes result in arbitrarily large values of the
 tilt dimensions, i.e. a dramatically deformed simulation box.  LAMMPS
 allows the tilt factors to grow a little beyond the normal limit of
-half the box length (0.6 times the box length), and then performs
+half the box length (0.6 times the box length), and then performs a
-flipping or re-shaping to an equivalent periodic cell. The re-shaping
+box "flip" to an equivalent periodic cell. The flip operation is
-operation is described in more detail in the doc page for "fix
+described in more detail in the doc page for "fix
 deform"_fix_deform.html.  Both the barostat dynamics and the atom
 trajectories are unaffected by this operation.  However, if a tilt
 factor is incremented by a large amount (1.5 times the box length) on
@@ -300,6 +300,13 @@ equilibrium liquids can not support a shear stress and that
 equilibrium solids can not support shear stresses that exceed the
 yield stress.
 
+The one exception to this rule is if the 1st dimension in the tilt
+factor (x for xy) is non-periodic.  In that case, the limits on the
+tilt factor are not enforced, since flipping the box in that dimension
+does not change the atom positions due to non-periodicity.  In this
+mode, if you tilt the system to extreme angles, the simulation will
+simply become inefficient due to the highly skewed simulation box.
+
 IMPORTANT NOTE: Unlike the "fix
 temp/berendsen"_fix_temp_berendsen.html command which performs
 thermostatting but NO time integration, these fixes perform
@@ -504,7 +511,8 @@ and if the tilt factor is not coupled to the barostat via keywords
   
 [Related commands:]
 
-"fix nve"_fix_nve.html, "fix_modify"_fix_modify.html, "run_style"_run_style.html
+"fix nve"_fix_nve.html, "fix_modify"_fix_modify.html,
+"run_style"_run_style.html
 
 [Default:]